hansenlab / bsseq

Devel repository for bsseq
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have problem with BS #63

Open zyworship opened 6 years ago

zyworship commented 6 years ago

list.files(pattern=".txt") -> report.files read.bismark(files=report.files,sampleNames=gsub(".txt","",report.files),rmZeroCov=TRUE, strandCollapse=FALSE,fileType="cytosineReporAssuming file type is cytosineReport Read 3547206 rows and 7 (of 7) columns from 0.107 GB file in 00:00:04 done in 9.7 secs Read 3547206 rows and 7 (of 7) columns from 0.107 GB file in 00:00:03 done in 6.7 secs [read.bismark] Reading file 'LZH369L_scaffold1.txt' ... done in 6.2 secs [read.bismark] Reading file 'LZH371L_scaffold1.txt' ... done in 6.5 secs [read.bismark] Reading file 'LZH373L_scaffold1.txt' ... done in 6.2 secs [read.bismark] Reading file 'MLS387L_scaffold1.txt' ... done in 6.4 secs [read.bismark] Reading file 'MLS388L_scaffold1.txt' ... done in 6.5 secs [read.bismark] Reading file 'MLS390L_scaffold1.txt' ... done in 6.3 secs [read.bismark] Joining samples ... done in 19.7 secs bsseq.data[[1]] <- c("high","low","low","low","low","high","high","high") bsseq.data[[2]] <- c("pair2","pair1","pair1","pair1","pair1","pair2","pair2","pair2") pData(bsseq.data) <- setNames(pData(bsseq.data),c("Type","pair")) bsseq.data.smoothed <- BSmooth(bsseq.data, verbose=TRUE) [BSmooth] preprocessing ... done in 2.6 sec [BSmooth] smoothing by 'sample' (mc.cores = 1, mc.preschedule = FALSE) [BSmooth] smoothing done in 91.9 sec Error in colnames<-(`tmp*`, value = c("HLiver_scaffold1", "LLiver_scaffold1", : attempt to set 'colnames' on an object with less than two dimensions I don't know the problem with this information.

PeteHaitch commented 6 years ago

I've seen this error when it runs out of memory. Can you successfully run fewer than 7 samples?

zyworship commented 6 years ago

@PeteHaitch I separated into scaffolds to run the bsseq, than it works. But I have another question. I apply for a 800G ram to run the total data, it has been read.bismark, but there is also reporting an error. This is my log file:

Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from ‘package:base’:

    apply

Assuming file type is cytosineReport
Error in .Call2("valid_Ranges", x_start, x_end, x_width, PACKAGE = "IRanges") :
  long vectors not supported yet: ../../../src/main/memory.c:3451
Calls: read.bismark ... anyStrings -> validityMethod -> valid.func -> .Call2 -> .Call
Execution halted

Have you met this error before ?

PeteHaitch commented 6 years ago

I have not seen this error. I have a suspicion what is causing it, but in order to investigate properly I really need a reproducible example.

Are you able to share one or more of your report.files to help me debug this error?

Please also post the output of sessionInfo() and BiocInstaller::biocValid() so I can see which package versions you are using.

zyworship commented 6 years ago

@PeteHaitch Thanks a lot, I try to give you a file ,but the report.files is to big, one file is more than 20gb. I am a little worry how to share the file with you. I have try run bsseq with scaffold, it run regularly and generate the dmr_file.

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/lib/libRblas.so
LAPACK: /GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] bsseq_1.14.0               SummarizedExperiment_1.8.1
 [3] DelayedArray_0.4.1         matrixStats_0.53.1
 [5] Biobase_2.38.0             GenomicRanges_1.30.3
 [7] GenomeInfoDb_1.14.0        IRanges_2.12.0
 [9] S4Vectors_0.16.0           BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16           XVector_0.18.0         zlibbioc_1.24.0
 [4] munsell_0.4.3          colorspace_1.3-2       lattice_0.20-35
 [7] plyr_1.8.4             tools_3.4.3            grid_3.4.3
[10] data.table_1.10.4-3    R.oo_1.21.0            gtools_3.5.0
[13] permute_0.9-4          Matrix_1.2-12          GenomeInfoDbData_1.0.0
[16] R.utils_2.6.0          bitops_1.0-6           RCurl_1.95-4.10
[19] limma_3.34.9           compiler_3.4.3         R.methodsS3_1.7.1
[22] scales_0.5.0           locfit_1.5-9.1
> BiocInstaller::biocValid()

* sessionInfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/lib/libRblas.so
LAPACK: /GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] bsseq_1.14.0               SummarizedExperiment_1.8.1
 [3] DelayedArray_0.4.1         matrixStats_0.53.1
 [5] Biobase_2.38.0             GenomicRanges_1.30.3
 [7] GenomeInfoDb_1.14.0        IRanges_2.12.0
 [9] S4Vectors_0.16.0           BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16           XVector_0.18.0         zlibbioc_1.24.0
 [4] munsell_0.4.3          colorspace_1.3-2       lattice_0.20-35
 [7] plyr_1.8.4             tools_3.4.3            grid_3.4.3
[10] data.table_1.10.4-3    R.oo_1.21.0            gtools_3.5.0
[13] permute_0.9-4          Matrix_1.2-12          GenomeInfoDbData_1.0.0
[16] R.utils_2.6.0          bitops_1.0-6           RCurl_1.95-4.10
[19] limma_3.34.9           BiocInstaller_1.28.0   compiler_3.4.3
[22] R.methodsS3_1.7.1      scales_0.5.0           locfit_1.5-9.1

* Out-of-date packages
                  Package
bindrcpp          "bindrcpp"
blob              "blob"
curl              "curl"
GenomicAlignments "GenomicAlignments"
monocle           "monocle"
plogr             "plogr"
proxy             "proxy"
RSQLite           "RSQLite"
viridis           "viridis"
                  LibPath
bindrcpp          "/GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/library"
blob              "/GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/library"
curl              "/GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/library"
GenomicAlignments "/GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/library"
monocle           "/GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/library"
plogr             "/GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/library"
proxy             "/GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/library"
RSQLite           "/GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/library"
viridis           "/GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/library"
                  Installed Built   ReposVer
bindrcpp          "0.2"     "3.4.3" "0.2.2"
blob              "1.1.0"   "3.4.3" "1.1.1"
curl              "3.1"     "3.4.3" "3.2"
GenomicAlignments "1.14.1"  "3.4.3" "1.14.2"
monocle           "2.6.3"   "3.4.3" "2.6.4"
plogr             "0.1-1"   "3.4.3" "0.2.0"
proxy             "0.4-21"  "3.4.3" "0.4-22"
RSQLite           "2.0"     "3.4.3" "2.1.0"
viridis           "0.5.0"   "3.4.3" "0.5.1"
                  Repository
bindrcpp          "https://cran.rstudio.com/src/contrib"
blob              "https://cran.rstudio.com/src/contrib"
curl              "https://cran.rstudio.com/src/contrib"
GenomicAlignments "https://bioconductor.org/packages/3.6/bioc/src/contrib"
monocle           "https://bioconductor.org/packages/3.6/bioc/src/contrib"
plogr             "https://cran.rstudio.com/src/contrib"
proxy             "https://cran.rstudio.com/src/contrib"
RSQLite           "https://cran.rstudio.com/src/contrib"
viridis           "https://cran.rstudio.com/src/contrib"

update with biocLite()

* Packages too new for Bioconductor version '3.6'

          Version LibPath
methylKit "1.5.2" "/GS01/software/biosoft/Rsoft/R3.4.3/lib64/R/library"

downgrade with biocLite("methylKit")

Error: 9 package(s) out of date; 1 package(s) too new
>
zyworship commented 6 years ago

@PeteHaitch I cut the header 2k line of one of my report.files like this:

scaffold1   3   -   0   0   CHH CTA
scaffold1   5   -   0   0   CHH CTC
scaffold1   7   -   0   0   CHH CTC
scaffold1   11  +   0   2   CHH CAA
scaffold1   15  -   0   1   CHH CTT
scaffold1   19  +   0   3   CHH CAT
scaffold1   23  -   0   1   CHH CAA
scaffold1   26  -   0   1   CHH CAA
scaffold1   32  +   0   3   CHH CAT
scaffold1   36  -   0   1   CHH CAA
scaffold1   39  +   0   3   CHG CAG
scaffold1   41  -   0   1   CHG CTG
scaffold1   42  -   0   1   CHH CCT
scaffold1   43  -   0   2   CHH CCC
scaffold1   44  -   0   2   CHH CCC
scaffold1   52  -   0   3   CHH CTT
scaffold1   53  +   0   3   CHH CAC
scaffold1   55  +   0   3   CHG CAG
scaffold1   57  -   0   5   CHG CTG
scaffold1   59  +   0   3   CHH CCT
scaffold1   60  +   0   3   CHH CTC
scaffold1   62  +   0   3   CHH CCT
scaffold1   63  +   0   3   CHG CTG
scaffold1   65  -   0   6   CHG CAG
scaffold1   66  +   0   3   CHH CCT
scaffold1   67  +   0   3   CHG CTG
scaffold1   69  -   0   6   CHG CAG
scaffold1   70  -   0   6   CHH CCA
scaffold1   71  -   0   6   CHH CCC
scaffold1   74  +   0   3   CHH CTC
scaffold1   76  +   0   3   CHH CAC
scaffold1   78  +   0   3   CHG CTG
scaffold1   80  -   0   6   CHG CAG
scaffold1   82  +   0   4   CHH CAA
scaffold1   86  -   0   6   CHH CAT
scaffold1   89  +   2   2   CG  CGG
scaffold1   90  -   4   2   CG  CGT
scaffold1   91  -   0   5   CHG CCG
scaffold1   93  -   0   6   CHH CTC
scaffold1   95  +   0   4   CHH CCT
scaffold1   96  +   0   4   CHH CTC
scaffold1   98  +   0   4   CHH CCA
scaffold1   99  +   0   4   CHH CAA
scaffold1   102 +   0   4   CHH CCC
scaffold1   103 +   0   4   CHH CCT
scaffold1   104 +   0   4   CHG CTG
scaffold1   106 -   0   6   CHG CAG
scaffold1   109 -   0   6   CHH CTT
scaffold1   110 +   0   4   CHH CTT
scaffold1   113 +   0   4   CHH CAT
scaffold1   116 -   0   6   CHH CAT
scaffold1   118 -   0   6   CHH CAC
scaffold1   120 +   0   4   CHH CAC
scaffold1   122 +   0   4   CHH CCC
scaffold1   123 +   0   4   CHH CCC
scaffold1   124 +   0   4   CHH CCT
scaffold1   125 +   0   4   CHH CTC
scaffold1   127 +   0   4   CHH CTT
scaffold1   130 +   0   4   CHH CCT
scaffold1   131 +   0   4   CHG CTG
scaffold1   133 -   0   7   CHG CAG
scaffold1   134 +   0   4   CHH CTT
scaffold1   137 +   0   4   CHH CCC
scaffold1   138 +   0   4   CHH CCT
scaffold1   139 +   0   4   CHH CTA
scaffold1   143 -   1   6   CHH CAT
scaffold1   146 -   0   7   CHH CTA
scaffold1   147 +   0   4   CHH CCC
scaffold1   148 +   0   4   CHH CCC
scaffold1   149 +   0   4   CHH CCA
scaffold1   150 +   0   4   CHG CAG
scaffold1   152 -   0   7   CHG CTG
scaffold1   154 -   0   7   CHH CAC
scaffold1   155 +   0   4   CHH CAA
scaffold1   159 -   0   8   CHH CAT
scaffold1   160 +   0   4   CHH CAA
scaffold1   164 -   0   8   CHH CAT
scaffold1   165 -   0   8   CHH CCA
scaffold1   167 -   0   8   CHH CTC
scaffold1   168 -   0   8   CHH CCT
scaffold1   169 +   0   4   CHG CTG
scaffold1   171 -   0   8   CHG CAG
scaffold1   175 -   0   8   CHH CAA
scaffold1   176 -   0   8   CHH CCA
scaffold1   178 +   0   4   CHH CCA
scaffold1   179 +   0   4   CHH CAT
scaffold1   182 -   0   8   CHH CAT
scaffold1   184 +   0   3   CHH CCC
scaffold1   185 +   0   3   CHH CCC
scaffold1   186 +   0   3   CHH CCC
scaffold1   187 +   0   3   CHH CCC
scaffold1   188 +   0   3   CHH CCT
scaffold1   189 +   0   3   CHH CTT
scaffold1   193 +   0   3   CHH CCC
scaffold1   194 +   1   2   CHH CCT
scaffold1   195 +   0   3   CHG CTG
scaffold1   197 -   0   8   CHG CAG
scaffold1   198 -   0   8   CHH CCA
scaffold1   200 -   0   8   CHH CTC
scaffold1   203 -   0   10  CHH CAT
scaffold1   204 +   0   3   CHH CTC
scaffold1   206 +   0   3   CHH CCA
scaffold1   207 +   0   3   CHH CAA
scaffold1   211 -   0   9   CHH CAT
scaffold1   212 -   0   9   CHH CCA
scaffold1   214 -   0   9   CHH CTC
scaffold1   215 -   0   9   CHH CCT
scaffold1   216 -   0   11  CHH CCC
scaffold1   225 -   1   11  CHH CAA
scaffold1   233 -   0   12  CHH CAA
scaffold1   237 +   0   4   CHH CAT
scaffold1   241 +   0   5   CHG CCG
scaffold1   242 +   3   2   CG  CGC
scaffold1   243 -   6   6   CG  CGG
scaffold1   244 +   0   5   CHH CCC
scaffold1   245 +   0   5   CHH CCT
scaffold1   246 +   0   5   CHH CTA
scaffold1   250 +   0   5   CHG CTG
scaffold1   252 -   0   11  CHG CAG
scaffold1   253 +   0   5   CHG CAG
scaffold1   255 -   0   11  CHG CTG
scaffold1   261 -   0   9   CHH CAA
scaffold1   262 +   0   6   CHH CTT
scaffold1   267 +   0   6   CHH CAC
scaffold1   269 +   0   6   CHH CAC
scaffold1   271 +   0   6   CHH CAT
scaffold1   276 -   0   9   CHH CAA
scaffold1   277 +   0   6   CHG CAG
scaffold1   279 -   1   9   CHG CTG
scaffold1   281 +   0   6   CHG CTG
scaffold1   283 -   1   8   CHG CAG
scaffold1   285 -   1   7   CHH CTC
scaffold1   288 -   1   7   CHH CTT
scaffold1   290 -   0   8   CHH CTC
scaffold1   294 -   1   7   CHH CAA
scaffold1   297 +   0   8   CHH CTC
scaffold1   299 +   0   8   CHG CTG
scaffold1   301 -   1   7   CHG CAG
scaffold1   303 +   0   8   CHH CAC
scaffold1   305 +   0   8   CHH CCT
scaffold1   306 +   0   8   CHG CTG
scaffold1   308 -   1   6   CHG CAG
scaffold1   309 +   0   8   CHG CCG
scaffold1   310 +   1   7   CG  CGG
scaffold1   311 -   2   5   CG  CGG
scaffold1   312 -   1   6   CHG CCG
scaffold1   315 -   1   7   CHH CTT
scaffold1   317 -   1   7   CHH CAC
scaffold1   318 -   1   8   CHH CCA
scaffold1   320 -   1   8   CHH CAC
scaffold1   323 -   1   8   CHH CTT
scaffold1   325 -   1   8   CHH CTC
scaffold1   328 +   0   10  CHH CTT
scaffold1   333 +   0   9   CHG CTG
scaffold1   335 -   1   6   CHG CAG
scaffold1   338 -   1   7   CHH CAT
scaffold1   339 +   0   12  CHG CAG
scaffold1   341 -   1   6   CHG CTG
scaffold1   346 -   1   5   CHH CAA
scaffold1   347 -   1   5   CHH CCA
scaffold1   350 +   0   12  CHH CCC
scaffold1   351 +   0   12  CHH CCC
scaffold1   352 +   0   12  CHH CCT
scaffold1   353 +   0   12  CHG CTG
scaffold1   355 -   1   5   CHG CAG
scaffold1   356 -   1   5   CHH CCA
scaffold1   359 -   0   6   CHH CTA
scaffold1   361 -   0   6   CHH CTC
scaffold1   362 -   0   7   CHH CCT
scaffold1   365 +   0   12  CHG CTG
scaffold1   367 -   0   7   CHG CAG
scaffold1   369 +   0   12  CHH CAT
scaffold1   372 +   0   12  CHH CAA
scaffold1   376 +   0   12  CHG CTG
scaffold1   378 -   1   6   CHG CAG
scaffold1   380 +   0   12  CHG CAG
scaffold1   382 -   1   6   CHG CTG
scaffold1   383 +   1   11  CG  CGT
scaffold1   384 -   1   6   CG  CGC
scaffold1   389 +   0   13  CHH CAC
scaffold1   391 +   0   13  CHH CAA
scaffold1   395 -   1   7   CHH CAT
scaffold1   396 +   1   12  CG  CGA
scaffold1   397 -   2   6   CG  CGC
scaffold1   399 -   1   6   CHH CTC
scaffold1   400 -   1   7   CHH CCT
scaffold1   402 -   1   7   CHH CAC
scaffold1   403 -   1   7   CHH CCA
scaffold1   404 -   0   8   CHH CCC
scaffold1   405 -   0   9   CHH CCC
scaffold1   406 -   0   9   CHH CCC
scaffold1   407 -   0   9   CHH CCC
scaffold1   409 -   0   9   CHH CAC
scaffold1   410 -   1   8   CHH CCA
scaffold1   411 -   0   9   CHH CCC
scaffold1   412 -   0   9   CHH CCC
scaffold1   413 -   0   10  CHH CCC
scaffold1   414 -   0   10  CHH CCC
scaffold1   416 -   0   10  CHH CTC
scaffold1   419 +   0   12  CHG CTG
scaffold1   421 -   1   9   CHG CAG
scaffold1   422 -   1   9   CHH CCA
scaffold1   423 +   1   12  CHG CTG
scaffold1   425 -   1   9   CHG CAG
scaffold1   426 +   0   11  CHH CAC
scaffold1   428 +   0   11  CHH CAT
scaffold1   433 +   0   12  CHH CAT
scaffold1   437 +   0   12  CHH CAC
scaffold1   439 +   0   12  CHH CCT
scaffold1   440 +   0   12  CHH CTC
scaffold1   442 +   0   12  CHH CTA
scaffold1   447 +   0   12  CHH CTC
scaffold1   449 +   0   12  CHH CTT
scaffold1   452 +   0   12  CHH CAT
scaffold1   456 -   1   11  CHH CAA
scaffold1   463 +   0   12  CHH CAT
scaffold1   470 +   0   12  CHG CCG
scaffold1   471 +   6   6   CG  CGC
scaffold1   472 -   6   6   CG  CGG
scaffold1   473 +   0   12  CHG CAG
scaffold1   475 -   1   11  CHG CTG
scaffold1   478 +   4   8   CG  CGA
scaffold1   479 -   5   8   CG  CGT
scaffold1   481 -   0   13  CHH CTC
scaffold1   482 -   1   12  CHH CCT
scaffold1   483 -   1   13  CHH CCC
scaffold1   484 -   0   14  CHH CCC
scaffold1   488 -   1   14  CHH CTT
scaffold1   490 +   0   11  CHH CTC
scaffold1   492 +   0   10  CHG CCG
scaffold1   493 +   4   6   CG  CGG
scaffold1   494 -   9   7   CG  CGG
scaffold1   495 -   1   15  CHG CCG
scaffold1   496 -   1   15  CHH CCC
scaffold1   501 +   0   9   CHH CCT
scaffold1   502 +   0   9   CHH CTC
scaffold1   504 +   0   9   CHG CTG
scaffold1   506 -   0   15  CHG CAG
scaffold1   508 -   0   15  CHH CTC
scaffold1   509 +   0   9   CHH CTT
scaffold1   512 +   0   9   CHH CAT
scaffold1   516 +   0   9   CHH CAA
scaffold1   519 +   0   8   CHH CCA
scaffold1   520 +   0   8   CHH CAA
scaffold1   528 -   0   13  CHH CTT
scaffold1   531 +   0   8   CHH CAA
scaffold1   538 -   0   15  CHH CTT
scaffold1   541 -   0   17  CHH CAT
scaffold1   543 +   1   8   CHH CAT
scaffold1   552 -   0   17  CHH CAT
scaffold1   553 -   0   17  CHH CCA
scaffold1   557 +   0   8   CHH CAC
scaffold1   559 +   1   5   CG  CGG
scaffold1   560 -   5   13  CG  CGT
scaffold1   561 -   0   18  CHG CCG
scaffold1   564 +   0   6   CHH CAC
scaffold1   566 +   0   6   CHH CAT
scaffold1   569 -   0   19  CHH CAT
scaffold1   571 -   1   18  CHH CTC
scaffold1   574 +   0   6   CHG CTG
scaffold1   576 -   1   16  CHG CAG
scaffold1   578 +   0   6   CHH CCC
scaffold1   579 +   0   6   CHH CCA
scaffold1   580 +   0   6   CHH CAA
scaffold1   583 +   0   6   CG  CGT
scaffold1   584 -   7   12  CG  CGT
scaffold1   586 -   1   18  CHH CAC
scaffold1   587 -   0   19  CHH CCA
scaffold1   588 +   0   4   CHH CTT
scaffold1   591 -   0   19  CHH CAA
scaffold1   595 -   0   19  CHH CAT
scaffold1   596 -   0   19  CHH CCA
scaffold1   598 -   0   19  CHH CAC
scaffold1   600 +   0   4   CHH CAT
scaffold1   605 +   0   4   CHH CTA
scaffold1   611 +   0   4   CHH CCT
scaffold1   612 +   0   4   CHH CTT
scaffold1   618 +   0   4   CHH CTA
scaffold1   621 +   0   5   CHH CTC
scaffold1   623 +   0   4   CHH CAC
scaffold1   625 +   0   5   CHH CAA
scaffold1   629 +   0   5   CHH CCA
scaffold1   630 +   0   5   CHH CAA
scaffold1   634 +   0   6   CHH CTA
scaffold1   637 -   0   20  CHH CTA
scaffold1   643 +   0   7   CHH CAA
scaffold1   647 +   0   7   CHH CAC
scaffold1   649 +   3   4   CG  CGA
scaffold1   650 -   10  9   CG  CGT
scaffold1   654 +   0   7   CHH CAC
scaffold1   656 +   0   6   CHG CAG
scaffold1   658 -   0   19  CHG CTG
scaffold1   659 +   0   6   CHH CTA
scaffold1   663 +   0   5   CHH CAC
scaffold1   665 +   0   5   CHH CAC
scaffold1   667 +   0   5   CHG CCG
scaffold1   668 +   2   3   CG  CGA
scaffold1   669 -   9   10  CG  CGG
scaffold1   671 -   0   19  CHH CTC
scaffold1   672 -   0   19  CHH CCT
scaffold1   674 -   0   19  CHH CAC
scaffold1   678 +   3   2   CG  CGG
scaffold1   679 -   8   9   CG  CGT
scaffold1   680 -   0   17  CHG CCG
scaffold1   683 +   0   5   CHH CCT
scaffold1   684 +   0   5   CHH CTC
scaffold1   686 +   0   5   CHG CAG
scaffold1   688 -   0   15  CHG CTG
scaffold1   690 +   0   6   CHH CAT
scaffold1   693 +   0   6   CHH CAT
scaffold1   696 +   0   6   CHG CAG
scaffold1   698 -   0   16  CHG CTG
scaffold1   700 +   0   6   CHH CCA
scaffold1   701 +   1   5   CHH CAA
scaffold1   705 -   0   16  CHH CTT
scaffold1   707 +   0   7   CHH CAT
scaffold1   710 +   3   4   CG  CGG
scaffold1   711 -   9   5   CG  CGA
scaffold1   712 -   0   14  CHG CCG
scaffold1   715 -   0   14  CHH CTT
scaffold1   718 +   0   6   CHH CTC
scaffold1   720 +   0   6   CHH CAA
scaffold1   724 +   0   6   CHH CAC
scaffold1   726 +   0   7   CHH CAA
scaffold1   729 -   0   14  CHH CTT
scaffold1   730 -   0   14  CHH CCT
scaffold1   731 +   0   9   CHH CTA
scaffold1   734 -   0   14  CHH CTA
scaffold1   742 -   0   12  CHH CTT
scaffold1   745 +   0   10  CHH CCC
scaffold1   746 +   0   10  CHH CCT
scaffold1   747 +   0   10  CHH CTA
scaffold1   752 +   0   10  CHH CTT
scaffold1   755 -   0   9   CHH CAA
scaffold1   756 -   0   9   CHH CCA
scaffold1   757 +   0   10  CHH CTA
scaffold1   762 -   0   5   CHH CTT
scaffold1   764 +   0   10  CHH CTT
scaffold1   767 -   0   5   CHH CAA
scaffold1   769 -   0   5   CHH CAC
scaffold1   774 -   0   5   CHH CAA
scaffold1   776 -   0   5   CHH CTC
scaffold1   779 +   0   10  CHG CAG
scaffold1   781 -   0   4   CHG CTG
scaffold1   785 -   0   4   CHH CAT
scaffold1   787 -   0   4   CHH CTC
scaffold1   788 -   0   4   CHH CCT
scaffold1   791 +   0   10  CHH CCC
scaffold1   792 +   0   10  CHH CCT
scaffold1   793 +   0   9   CHG CTG
scaffold1   795 -   0   5   CHG CAG
scaffold1   797 -   0   5   CHH CTC
scaffold1   798 -   0   5   CHH CCT
scaffold1   799 -   0   5   CHH CCC
scaffold1   800 -   0   5   CHH CCC
scaffold1   805 +   0   9   CHH CAT
scaffold1   808 -   0   5   CHH CAT
scaffold1   811 -   0   5   CHH CAT
scaffold1   812 -   0   5   CHH CCA
scaffold1   814 -   0   6   CHH CTC
scaffold1   815 -   0   7   CHH CCT
scaffold1   820 +   0   9   CHH CTT
scaffold1   827 +   0   10  CHH CCC
scaffold1   828 +   1   9   CHG CCG
scaffold1   829 +   9   1   CG  CGT
scaffold1   830 -   5   1   CG  CGG
scaffold1   832 -   0   6   CHH CAC
scaffold1   833 -   0   5   CHH CCA
scaffold1   836 +   0   10  CHH CTC
scaffold1   838 +   0   10  CHH CAA
scaffold1   841 +   0   10  CHG CTG
scaffold1   843 -   0   6   CHG CAG
scaffold1   844 -   0   6   CHH CCA
scaffold1   846 -   0   6   CHH CAC
scaffold1   847 -   0   6   CHH CCA
scaffold1   848 -   0   6   CHH CCC
scaffold1   850 +   0   10  CHH CAT
scaffold1   853 -   0   6   CHH CAT
scaffold1   855 +   0   8   CHH CCC
scaffold1   856 +   0   8   CHH CCA
scaffold1   857 +   0   8   CHG CAG
scaffold1   859 -   0   7   CHG CTG
scaffold1   862 -   0   7   CHH CTT
scaffold1   864 -   0   7   CHH CAC
scaffold1   865 -   0   7   CHH CCA
scaffold1   866 -   0   8   CHH CCC
scaffold1   868 +   6   2   CG  CGC
scaffold1   869 -   7   1   CG  CGA
scaffold1   870 +   7   0   CG  CGG
scaffold1   871 -   8   0   CG  CGC
scaffold1   872 -   0   8   CHG CCG
scaffold1   874 +   0   7   CHH CCC
scaffold1   875 +   0   7   CHH CCA
scaffold1   876 +   0   7   CHH CAT
scaffold1   879 -   0   7   CHH CAT
scaffold1   882 +   0   9   CHG CTG
scaffold1   884 -   0   7   CHG CAG
scaffold1   886 -   0   7   CHH CAC
scaffold1   887 -   0   7   CHH CCA
scaffold1   888 -   1   6   CHH CCC
scaffold1   890 +   0   9   CHH CAC
scaffold1   892 +   0   9   CHG CCG
scaffold1   893 +   8   1   CG  CGC
scaffold1   894 -   6   1   CG  CGG
scaffold1   895 +   0   9   CHH CAT
scaffold1   898 -   0   7   CHH CAT
scaffold1   899 +   0   9   CHH CCT
scaffold1   900 +   0   9   CHH CTT
scaffold1   903 +   0   9   CHH CCA
scaffold1   904 +   0   9   CHH CAC
scaffold1   906 +   0   9   CHG CTG
scaffold1   908 -   1   5   CHG CAG
scaffold1   909 +   0   9   CHH CAC
scaffold1   911 +   0   9   CHH CTA
scaffold1   914 -   0   6   CHH CTA
scaffold1   917 -   0   5   CHH CAT
scaffold1   919 -   0   5   CHH CTC
scaffold1   921 -   0   5   CHH CTC
scaffold1   922 -   0   5   CHH CCT
scaffold1   925 +   0   9   CHH CCT
scaffold1   926 +   0   9   CHH CTC
scaffold1   928 +   0   9   CHG CAG
scaffold1   930 -   0   7   CHG CTG
scaffold1   931 +   0   9   CHH CCC
scaffold1   932 +   0   9   CHH CCC
scaffold1   933 +   0   8   CHH CCC
scaffold1   934 +   0   8   CHH CCC
scaffold1   935 +   0   8   CHH CCT
scaffold1   936 +   0   8   CHH CTC
scaffold1   938 +   0   8   CHH CCA
scaffold1   939 +   0   8   CHH CAT
scaffold1   945 -   0   5   CHH CAT
scaffold1   946 +   0   8   CHH CAT
scaffold1   949 +   6   1   CG  CGC
scaffold1   950 -   5   1   CG  CGA
scaffold1   951 +   0   7   CHG CTG
scaffold1   953 -   0   6   CHG CAG
scaffold1   955 -   0   6   CHH CAC
scaffold1   959 -   0   6   CHH CTA
scaffold1   960 -   0   6   CHH CCT
scaffold1   961 +   0   6   CHG CCG
scaffold1   962 +   6   0   CG  CGC
scaffold1   963 -   6   0   CG  CGG
scaffold1   964 +   0   7   CHH CCT
scaffold1   965 +   1   6   CHG CTG
scaffold1   967 -   0   6   CHG CAG
scaffold1   968 -   0   6   CHH CCA
scaffold1   969 +   5   1   CG  CGC
scaffold1   970 -   6   0   CG  CGC
scaffold1   971 +   0   6   CHG CTG
scaffold1   973 -   0   6   CHG CAG
scaffold1   977 -   0   6   CHH CAA
scaffold1   979 +   0   8   CHG CAG
scaffold1   981 -   0   6   CHG CTG
scaffold1   982 +   0   8   CHH CTT
scaffold1   986 -   0   7   CHH CTA
scaffold1   987 -   0   7   CHH CCT
scaffold1   988 -   0   7   CHH CCC
scaffold1   990 -   0   7   CHH CAC
scaffold1   991 -   0   7   CHH CCA
scaffold1   992 -   0   7   CHH CCC
scaffold1   993 +   0   8   CHG CTG
scaffold1   995 -   0   6   CHG CAG
scaffold1   996 -   0   7   CHH CCA
scaffold1   997 -   0   7   CHH CCC
scaffold1   998 -   0   7   CHH CCC
scaffold1   1003    -   0   7   CHH CAT
scaffold1   1004    -   0   7   CHH CCA
scaffold1   1005    +   0   7   CHG CCG
scaffold1   1006    +   5   1   CG  CGG
scaffold1   1007    -   6   1   CG  CGG
scaffold1   1008    -   0   7   CHG CCG
scaffold1   1009    -   0   7   CHH CCC
scaffold1   1011    -   0   7   CHH CTC
scaffold1   1012    -   0   7   CHH CCT
scaffold1   1013    -   0   7   CHH CCC
scaffold1   1015    -   0   7   CHH CTC
scaffold1   1016    +   0   6   CHH CTC
scaffold1   1018    +   0   6   CHH CCA
scaffold1   1019    +   0   6   CHH CAT
scaffold1   1023    +   0   6   CHH CAT
scaffold1   1027    +   0   6   CHH CCT
scaffold1   1028    +   0   6   CHG CTG
scaffold1   1030    -   0   7   CHG CAG
scaffold1   1031    +   0   6   CHH CAT
scaffold1   1035    -   0   7   CHH CAA
scaffold1   1036    +   0   6   CHH CTT
scaffold1   1042    -   0   7   CHH CTA
scaffold1   1043    +   0   6   CHH CTC
scaffold1   1045    +   0   6   CHH CCC
scaffold1   1046    +   0   6   CHH CCT
scaffold1   1047    +   0   6   CHH CTC
scaffold1   1049    +   4   2   CG  CGC
scaffold1   1050    -   7   0   CG  CGA
scaffold1   1051    +   0   6   CHH CCT
scaffold1   1052    +   0   6   CHG CTG
scaffold1   1054    -   0   7   CHG CAG
scaffold1   1056    +   0   6   CHH CAA
scaffold1   1059    +   0   6   CHH CAC
scaffold1   1061    +   0   6   CHH CAT
scaffold1   1065    -   0   7   CHH CAA
scaffold1   1067    -   0   7   CHH CAC
scaffold1   1068    -   0   7   CHH CCA
scaffold1   1069    +   0   5   CHH CTC
scaffold1   1071    +   0   5   CHH CCC
scaffold1   1072    +   0   5   CHH CCA
scaffold1   1073    +   0   5   CHH CAC
scaffold1   1075    +   0   5   CHH CCA
scaffold1   1076    +   0   5   CHH CAC
scaffold1   1078    +   0   5   CHH CCT
scaffold1   1079    +   0   5   CHH CTC
scaffold1   1081    +   0   5   CHH CTA
scaffold1   1084    +   0   5   CHG CAG
scaffold1   1086    -   0   5   CHG CTG
scaffold1   1087    -   0   5   CHH CCT
scaffold1   1088    -   0   5   CHH CCC
scaffold1   1090    -   0   4   CHH CTC
scaffold1   1092    -   0   4   CHH CAC
scaffold1   1093    +   0   4   CHH CAA
scaffold1   1096    -   0   4   CHH CTT
scaffold1   1097    -   0   4   CHH CCT
scaffold1   1098    -   0   4   CHH CCC
scaffold1   1101    +   0   2   CHG CTG
scaffold1   1103    -   0   3   CHG CAG
scaffold1   1106    +   0   2   CHH CAA
scaffold1   1109    -   0   3   CHH CTT
scaffold1   1110    +   0   2   CHH CAA
scaffold1   1114    -   0   3   CHH CAT
scaffold1   1115    +   0   2   CHH CAA
scaffold1   1118    -   0   3   CHH CTT
scaffold1   1122    -   0   3   CHH CAT
scaffold1   1123    -   0   3   CHH CCA
scaffold1   1126    -   0   2   CHH CAT
scaffold1   1129    -   0   2   CHH CTA
scaffold1   1130    +   0   2   CHH CTC
scaffold1   1132    +   0   2   CHH CCA
scaffold1   1133    +   0   2   CHH CAT
scaffold1   1136    +   0   2   CHH CAC
scaffold1   1138    +   0   2   CHG CAG
scaffold1   1140    -   0   2   CHG CTG
scaffold1   1143    +   0   2   CHG CAG
scaffold1   1145    -   0   2   CHG CTG
scaffold1   1146    +   0   2   CHG CAG
scaffold1   1148    -   0   2   CHG CTG
scaffold1   1149    +   0   1   CHH CCC
scaffold1   1150    +   0   1   CHH CCA
scaffold1   1151    +   0   1   CHH CAC
scaffold1   1153    +   0   1   CHH CAC
scaffold1   1155    +   0   1   CHH CTA
scaffold1   1158    +   0   1   CHH CAC
scaffold1   1160    +   0   1   CHH CCT
scaffold1   1161    +   0   1   CHH CTC
scaffold1   1163    +   0   1   CHH CTA
scaffold1   1170    -   0   1   CHH CAT
scaffold1   1171    -   0   1   CHH CCA
scaffold1   1172    -   0   1   CHH CCC
scaffold1   1173    -   0   1   CHH CCC
scaffold1   1174    -   0   1   CHH CCC
scaffold1   1175    -   0   1   CHH CCC
scaffold1   1176    -   0   1   CHH CCC
scaffold1   1177    -   0   1   CHH CCC
scaffold1   1178    -   0   1   CHH CCC
scaffold1   1179    -   0   1   CHH CCC
scaffold1   1180    -   0   1   CHH CCC
scaffold1   1181    -   0   1   CHH CCC
scaffold1   1185    -   0   2   CHH CAT
scaffold1   1187    -   0   2   CHH CAC
scaffold1   1189    -   0   2   CHH CAC
scaffold1   1191    -   0   3   CHH CAC
scaffold1   1193    -   0   3   CHH CAC
scaffold1   1195    -   0   3   CHH CTC
scaffold1   1199    -   0   3   CHH CAA
scaffold1   1201    -   0   3   CHH CAC
scaffold1   1203    +   0   1   CHG CTG
scaffold1   1205    -   0   3   CHG CAG
scaffold1   1207    +   0   1   CHG CAG
scaffold1   1209    -   0   3   CHG CTG
scaffold1   1211    -   0   3   CHH CAC
scaffold1   1219    +   0   2   CHH CAC
scaffold1   1221    +   0   2   CHH CAA
scaffold1   1225    +   0   2   CHH CTA
scaffold1   1228    +   0   2   CHH CTA
scaffold1   1231    +   2   0   CG  CGC
scaffold1   1232    -   4   0   CG  CGT
scaffold1   1233    +   0   2   CHH CAA
scaffold1   1237    +   0   3   CHH CAC
scaffold1   1239    +   0   3   CHH CAC
scaffold1   1241    +   0   3   CHH CCT
scaffold1   1242    +   0   3   CHH CTA
scaffold1   1245    +   0   3   CHG CTG
scaffold1   1247    -   0   4   CHG CAG
scaffold1   1248    +   0   3   CHH CTC
scaffold1   1250    +   0   3   CHH CAT
scaffold1   1254    +   0   3   CHG CTG
scaffold1   1256    -   0   4   CHG CAG
scaffold1   1257    -   0   4   CHH CCA
scaffold1   1259    -   0   4   CHH CAC
scaffold1   1261    -   0   4   CHH CAC
scaffold1   1263    -   0   4   CHH CTC
scaffold1   1265    -   0   4   CHH CTC
scaffold1   1266    -   0   4   CHH CCT
scaffold1   1268    -   0   4   CHH CAC
scaffold1   1269    +   3   0   CG  CGT
scaffold1   1270    -   4   1   CG  CGC
scaffold1   1273    -   0   5   CHH CAA
scaffold1   1274    +   3   0   CG  CGT
scaffold1   1275    -   4   1   CG  CGC
scaffold1   1278    -   0   6   CHH CAA
scaffold1   1279    +   3   0   CG  CGT
scaffold1   1280    -   5   2   CG  CGC
scaffold1   1283    -   0   7   CHH CAA
scaffold1   1284    +   0   3   CHG CCG
scaffold1   1285    +   3   0   CG  CGT
scaffold1   1286    -   6   1   CG  CGG
scaffold1   1289    +   0   5   CHH CAT
scaffold1   1298    -   0   7   CHH CAA
scaffold1   1299    -   0   7   CHH CCA
scaffold1   1300    +   0   7   CHH CAC
scaffold1   1302    +   0   7   CHH CCC
scaffold1   1303    +   0   7   CHH CCC
scaffold1   1304    +   0   7   CHH CCA
scaffold1   1305    +   0   7   CHH CAA
scaffold1   1311    +   0   8   CHH CAC
scaffold1   1313    +   0   8   CHH CCT
scaffold1   1314    +   0   8   CHH CTC
scaffold1   1316    +   0   8   CHH CTC
scaffold1   1318    +   7   1   CG  CGC
scaffold1   1319    -   7   1   CG  CGA
scaffold1   1320    +   0   8   CHH CAC
scaffold1   1322    +   0   8   CHH CAC
scaffold1   1324    +   0   8   CHG CAG
scaffold1   1326    -   0   8   CHG CTG
scaffold1   1330    -   0   8   CHH CAA
scaffold1   1331    -   0   8   CHH CCA
scaffold1   1332    +   0   8   CHG CTG
scaffold1   1334    -   0   8   CHG CAG
scaffold1   1336    -   0   8   CHH CAC
scaffold1   1338    -   0   8   CHH CAC
scaffold1   1339    +   0   8   CHH CAC
scaffold1   1341    +   0   8   CHG CCG
scaffold1   1342    +   6   2   CG  CGG
scaffold1   1343    -   7   1   CG  CGG
scaffold1   1344    -   0   8   CHG CCG
scaffold1   1347    +   0   8   CHH CAT
scaffold1   1350    -   1   7   CHH CAT
scaffold1   1351    +   8   0   CG  CGG
scaffold1   1352    -   8   1   CG  CGC
scaffold1   1353    -   0   9   CHG CCG
scaffold1   1356    +   0   8   CHG CCG
scaffold1   1357    +   7   1   CG  CGC
scaffold1   1358    -   9   0   CG  CGG
scaffold1   1359    +   0   8   CHH CAA
scaffold1   1363    -   0   8   CHH CAT
scaffold1   1364    +   0   8   CHG CCG
scaffold1   1365    +   7   1   CG  CGT
scaffold1   1366    -   8   0   CG  CGG
scaffold1   1368    -   0   8   CHH CAC
scaffold1   1370    -   2   6   CHH CAC
scaffold1   1371    +   0   7   CHH CTC
scaffold1   1373    +   0   8   CHH CCA
scaffold1   1374    +   0   8   CHG CAG
scaffold1   1376    -   0   8   CHG CTG
scaffold1   1378    -   0   9   CHH CAC
scaffold1   1380    -   0   9   CHH CAC
scaffold1   1383    -   0   9   CHH CTA
scaffold1   1384    +   8   1   CG  CGA
scaffold1   1385    -   8   1   CG  CGC
scaffold1   1387    +   0   9   CHH CAT
scaffold1   1390    -   0   11  CHH CAT
scaffold1   1391    -   0   11  CHH CCA
scaffold1   1392    -   0   11  CHH CCC
scaffold1   1394    +   8   1   CG  CGT
scaffold1   1395    -   10  1   CG  CGA
scaffold1   1397    -   0   12  CHH CAC
scaffold1   1399    +   0   9   CHH CTT
scaffold1   1403    -   1   12  CHH CTA
scaffold1   1405    -   0   12  CHH CAC
scaffold1   1407    +   0   9   CHH CCA
scaffold1   1408    +   0   9   CHH CAA
scaffold1   1411    -   0   13  CHH CTT
scaffold1   1412    -   0   14  CHH CCT
scaffold1   1413    -   0   14  CHH CCC
scaffold1   1414    +   0   8   CHH CAA
scaffold1   1419    -   0   14  CHH CAT
scaffold1   1421    -   0   14  CHH CAC
scaffold1   1422    -   0   14  CHH CCA
scaffold1   1423    -   0   14  CHH CCC
scaffold1   1425    +   0   8   CHH CCT
scaffold1   1426    +   0   8   CHG CTG
scaffold1   1428    -   0   14  CHG CAG
scaffold1   1429    +   8   0   CG  CGG
scaffold1   1430    -   14  3   CG  CGC
scaffold1   1431    -   0   18  CHG CCG
scaffold1   1437    +   0   8   CHG CAG
scaffold1   1439    -   0   19  CHG CTG
scaffold1   1440    -   1   18  CHH CCT
scaffold1   1443    -   0   19  CHH CAA
scaffold1   1445    -   0   19  CHH CTC
scaffold1   1448    +   0   10  CHH CCA
scaffold1   1449    +   1   9   CHH CAT
scaffold1   1454    +   1   9   CHG CAG
scaffold1   1456    -   0   19  CHG CTG
scaffold1   1457    -   0   19  CHH CCT
scaffold1   1458    +   0   12  CHG CTG
scaffold1   1460    -   0   19  CHG CAG
scaffold1   1461    -   0   19  CHH CCA
scaffold1   1462    -   0   19  CHH CCC
scaffold1   1465    -   1   19  CHH CTT
scaffold1   1466    -   0   21  CHH CCT
scaffold1   1467    -   0   21  CHH CCC
scaffold1   1468    +   0   12  CHH CTC
scaffold1   1470    +   0   13  CHH CCC
scaffold1   1471    +   0   13  CHG CCG
scaffold1   1472    +   13  0   CG  CGT
scaffold1   1473    -   18  2   CG  CGG
scaffold1   1475    +   12  1   CG  CGT
scaffold1   1476    -   14  6   CG  CGA
scaffold1   1478    -   0   19  CHH CAC
scaffold1   1480    +   0   13  CHH CCC
scaffold1   1481    +   0   13  CHH CCT
scaffold1   1482    +   2   11  CHH CTT
scaffold1   1485    -   1   18  CHH CAA
scaffold1   1486    -   0   19  CHH CCA
scaffold1   1488    -   0   20  CHH CAC
scaffold1   1490    +   0   12  CHH CCT
scaffold1   1491    +   0   12  CHH CTC
scaffold1   1493    +   0   13  CHH CAC
scaffold1   1495    +   0   14  CHG CTG
scaffold1   1497    -   0   19  CHG CAG
scaffold1   1498    -   0   20  CHH CCA
scaffold1   1499    -   0   20  CHH CCC
scaffold1   1500    -   0   20  CHH CCC
scaffold1   1502    -   0   20  CHH CTC
scaffold1   1503    -   0   20  CHH CCT
scaffold1   1506    -   0   20  CHH CTT
scaffold1   1509    -   0   20  CHH CAA
scaffold1   1513    -   0   18  CHH CAT
scaffold1   1515    +   0   14  CHH CCT
scaffold1   1516    +   0   14  CHH CTT
scaffold1   1519    +   0   13  CHG CAG
scaffold1   1521    -   0   17  CHG CTG
scaffold1   1524    +   1   11  CHH CAT
scaffold1   1527    +   10  1   CG  CGG
scaffold1   1528    -   13  2   CG  CGA
scaffold1   1529    -   0   15  CHG CCG
scaffold1   1531    +   0   11  CHH CCC
scaffold1   1532    +   0   11  CHH CCC
scaffold1   1533    +   0   11  CHH CCT
scaffold1   1534    +   0   11  CHH CTC
scaffold1   1536    +   0   11  CHG CAG
scaffold1   1538    -   0   15  CHG CTG
scaffold1   1545    -   0   15  CHH CAT
scaffold1   1551    +   0   11  CHH CTC
scaffold1   1553    +   9   2   CG  CGG
scaffold1   1554    -   9   2   CG  CGA
scaffold1   1555    -   0   10  CHG CCG
scaffold1   1560    +   0   11  CHH CTT
scaffold1   1564    +   0   11  CHG CAG
scaffold1   1566    -   0   10  CHG CTG
scaffold1   1567    -   0   10  CHH CCT
scaffold1   1569    -   0   10  CHH CAC
scaffold1   1571    +   0   10  CHH CTC
scaffold1   1573    +   0   10  CHG CCG
scaffold1   1574    +   10  0   CG  CGG
scaffold1   1575    -   10  0   CG  CGG
scaffold1   1576    -   0   10  CHG CCG
scaffold1   1578    -   0   10  CHH CAC
scaffold1   1581    -   0   11  CHH CTT
scaffold1   1582    -   0   11  CHH CCT
scaffold1   1585    +   0   11  CHG CTG
scaffold1   1587    -   0   11  CHG CAG
scaffold1   1588    -   0   10  CHH CCA
scaffold1   1590    -   0   10  CHH CAC
scaffold1   1593    +   0   11  CHH CCT
scaffold1   1594    +   0   11  CHH CTC
scaffold1   1596    +   0   11  CHH CCA
scaffold1   1597    +   0   11  CHH CAT
scaffold1   1600    +   1   10  CHH CAT
scaffold1   1604    +   0   13  CHH CAA
scaffold1   1608    -   0   12  CHH CTT
scaffold1   1610    +   0   13  CHH CAT
scaffold1   1614    -   0   11  CHH CAA
scaffold1   1615    +   0   12  CHG CAG
scaffold1   1617    -   1   10  CHG CTG
scaffold1   1619    +   0   11  CHH CAA
scaffold1   1624    -   0   10  CHH CAA
scaffold1   1626    -   0   10  CHH CAC
scaffold1   1627    +   0   11  CHH CTC
scaffold1   1629    +   0   10  CHH CTT
scaffold1   1632    +   0   10  CHH CCA
scaffold1   1633    +   1   9   CHG CAG
scaffold1   1635    -   0   9   CHG CTG
scaffold1   1636    +   0   10  CHH CCT
scaffold1   1637    +   0   10  CHH CTT
scaffold1   1640    -   0   9   CHH CAA
scaffold1   1642    -   0   9   CHH CAC
scaffold1   1643    -   0   9   CHH CCA
scaffold1   1645    +   0   10  CHH CAC
scaffold1   1647    +   0   10  CHG CAG
scaffold1   1649    -   0   9   CHG CTG
scaffold1   1653    -   0   9   CHH CAA
scaffold1   1654    -   0   9   CHH CCA
scaffold1   1656    -   0   8   CHH CAC
scaffold1   1659    -   0   6   CHH CTT
scaffold1   1661    +   0   9   CHH CCC
scaffold1   1662    +   0   9   CHH CCT
scaffold1   1663    +   0   9   CHH CTT
scaffold1   1668    +   0   8   CHG CTG
scaffold1   1670    -   0   5   CHG CAG
scaffold1   1672    +   0   8   CHH CCC
scaffold1   1673    +   0   8   CHH CCC
scaffold1   1674    +   0   8   CHH CCC
scaffold1   1675    +   0   8   CHH CCC
scaffold1   1676    +   0   8   CHH CCC
scaffold1   1677    +   0   8   CHH CCA
scaffold1   1678    +   0   8   CHH CAT
scaffold1   1681    -   0   5   CHH CAT
scaffold1   1683    +   0   7   CHG CTG
scaffold1   1685    -   0   5   CHG CAG
scaffold1   1687    +   0   7   CHH CCC
scaffold1   1688    +   0   7   CHH CCC
scaffold1   1689    +   0   7   CHH CCC
scaffold1   1690    +   0   7   CHH CCA
scaffold1   1691    +   0   7   CHH CAT
scaffold1   1694    -   0   7   CHH CAT
scaffold1   1697    +   0   9   CHH CAA
scaffold1   1701    -   0   7   CHH CTT
scaffold1   1702    +   0   8   CHH CCA
scaffold1   1703    +   1   7   CHG CAG
scaffold1   1705    -   0   6   CHG CTG
scaffold1   1706    +   0   8   CHH CTC
scaffold1   1708    +   0   8   CHH CCA
scaffold1   1709    +   0   8   CHH CAT
scaffold1   1713    +   0   8   CHG CAG
scaffold1   1715    -   0   6   CHG CTG
scaffold1   1720    -   0   6   CHH CAT
scaffold1   1721    -   0   6   CHH CCA
scaffold1   1723    -   0   6   CHH CAC
scaffold1   1725    -   0   6   CHH CAC
scaffold1   1727    +   0   8   CHH CCA
scaffold1   1728    +   0   8   CHG CAG
scaffold1   1730    -   0   5   CHG CTG
scaffold1   1732    -   0   5   CHH CAC
scaffold1   1734    -   0   5   CHH CAC
scaffold1   1735    -   0   5   CHH CCA
scaffold1   1737    -   0   6   CHH CAC
scaffold1   1738    -   0   6   CHH CCA
scaffold1   1740    -   0   7   CHH CTC
scaffold1   1741    -   0   7   CHH CCT
scaffold1   1744    +   0   8   CHH CTC
scaffold1   1746    +   5   4   CG  CGA
scaffold1   1747    -   6   1   CG  CGA
scaffold1   1749    -   0   7   CHH CTC
scaffold1   1751    -   0   8   CHH CAC
scaffold1   1753    +   0   9   CHH CCT
scaffold1   1754    +   0   9   CHG CTG
scaffold1   1756    -   0   8   CHG CAG
scaffold1   1758    -   0   8   CHH CTC
scaffold1   1759    +   0   9   CHG CAG
scaffold1   1761    -   0   7   CHG CTG
scaffold1   1763    -   0   8   CHH CTC
scaffold1   1764    +   0   9   CHH CCC
scaffold1   1765    +   0   9   CHH CCT
scaffold1   1766    +   0   9   CHG CTG
scaffold1   1768    -   0   9   CHG CAG
scaffold1   1770    +   0   9   CHH CCT
scaffold1   1771    +   0   9   CHH CTC
scaffold1   1773    +   0   8   CHH CAT
scaffold1   1776    +   0   8   CHH CCC
scaffold1   1777    +   0   8   CHH CCT
scaffold1   1778    +   0   8   CHH CTA
scaffold1   1781    +   0   8   CHG CTG
scaffold1   1783    -   0   9   CHG CAG
scaffold1   1786    +   0   8   CHH CAC
scaffold1   1788    +   0   8   CHH CCT
scaffold1   1789    +   0   8   CHH CTT
scaffold1   1793    -   0   9   CHH CAA
scaffold1   1794    -   0   9   CHH CCA
scaffold1   1795    -   0   9   CHH CCC
scaffold1   1796    -   1   8   CHH CCC
scaffold1   1798    -   0   10  CHH CAC
scaffold1   1803    -   0   10  CHH CAA
scaffold1   1804    -   0   10  CHH CCA
scaffold1   1805    -   0   10  CHH CCC
scaffold1   1807    +   0   10  CHH CCC
scaffold1   1808    +   0   10  CHH CCT
scaffold1   1809    +   0   10  CHG CTG
scaffold1   1811    -   0   11  CHG CAG
scaffold1   1815    -   0   11  CHH CAA
scaffold1   1817    -   0   11  CHH CAC
scaffold1   1819    -   0   12  CHH CTC
scaffold1   1820    +   0   9   CHH CCT
scaffold1   1821    +   0   9   CHG CTG
scaffold1   1823    -   0   12  CHG CAG
scaffold1   1824    -   0   13  CHH CCA
scaffold1   1826    +   0   7   CHH CTT
scaffold1   1829    +   0   7   CHH CTC
scaffold1   1831    +   0   7   CHH CAC
scaffold1   1833    +   0   7   CHH CCC
scaffold1   1834    +   0   7   CHH CCA
scaffold1   1835    +   0   7   CHH CAA
scaffold1   1838    +   0   8   CHH CAT
scaffold1   1841    +   0   8   CHG CAG
scaffold1   1843    -   0   13  CHG CTG
scaffold1   1846    +   0   8   CHH CCT
scaffold1   1847    +   0   8   CHG CTG
scaffold1   1849    -   0   14  CHG CAG
scaffold1   1852    -   0   14  CHH CTT
scaffold1   1854    -   0   14  CHH CTC
scaffold1   1855    -   0   14  CHH CCT
scaffold1   1856    -   0   14  CHH CCC
scaffold1   1867    -   1   14  CHH CTT
scaffold1   1868    -   0   15  CHH CCT
scaffold1   1871    -   0   15  CHH CAT
scaffold1   1872    +   0   9   CHH CCA
scaffold1   1873    +   0   8   CHH CAT
scaffold1   1877    +   5   2   CG  CGT
scaffold1   1878    -   14  0   CG  CGT
scaffold1   1881    -   0   13  CHH CTA
scaffold1   1883    -   0   14  CHH CTC
scaffold1   1885    -   1   13  CHH CAC
scaffold1   1889    -   0   14  CHH CAT
scaffold1   1891    -   0   15  CHH CTC
scaffold1   1894    -   0   16  CHH CTT
scaffold1   1895    +   0   6   CHH CTT
scaffold1   1902    +   0   7   CHH CTC
scaffold1   1904    +   0   7   CHH CCA
scaffold1   1905    +   0   7   CHH CAA
scaffold1   1908    +   0   7   CHG CAG
scaffold1   1910    -   0   16  CHG CTG
scaffold1   1912    -   1   15  CHH CAC
scaffold1   1915    -   0   16  CHH CAT
scaffold1   1917    -   0   15  CHH CAC
scaffold1   1920    +   0   6   CHH CCC
scaffold1   1921    +   0   6   CHH CCA
scaffold1   1922    +   0   6   CHH CAA
scaffold1   1925    +   0   6   CHH CAT
scaffold1   1928    +   0   6   CHH CCA
scaffold1   1929    +   0   6   CHH CAT
scaffold1   1932    -   1   14  CHH CAT
scaffold1   1933    -   0   15  CHH CCA
scaffold1   1936    -   1   13  CHH CAA
scaffold1   1937    +   0   5   CHH CCA
scaffold1   1938    +   0   5   CHH CAC
scaffold1   1940    +   0   5   CHH CCT
scaffold1   1941    +   0   5   CHG CTG
scaffold1   1943    -   0   15  CHG CAG
scaffold1   1945    +   0   5   CHH CCA
scaffold1   1946    +   0   5   CHH CAT
scaffold1   1949    +   0   5   CHH CAC
scaffold1   1951    +   0   5   CHH CAC
scaffold1   1953    +   0   5   CHH CCT
scaffold1   1954    +   0   5   CHH CTA
scaffold1   1957    +   0   5   CHH CCT
scaffold1   1958    +   0   5   CHH CTA
scaffold1   1964    -   0   14  CHH CAT
scaffold1   1967    +   0   6   CHG CAG
scaffold1   1969    -   0   15  CHG CTG
scaffold1   1972    +   0   6   CHH CTA
scaffold1   1978    -   0   15  CHH CAA
scaffold1   1979    -   0   15  CHH CCA
scaffold1   1981    +   0   6   CHH CCC
scaffold1   1982    +   0   6   CHH CCT
scaffold1   1983    +   0   6   CHH CTC
scaffold1   1985    +   0   6   CHH CCT
scaffold1   1986    +   0   6   CHH CTC
scaffold1   1988    +   0   6   CHH CCT
scaffold1   1989    +   0   6   CHH CTA
scaffold1   1994    -   0   15  CHH CAT
scaffold1   1997    -   0   16  CHH CAT
scaffold1   1998    -   0   16  CHH CCA
scaffold1   2000    -   0   16  CHH CTC
scaffold1   2003    +   0   6   CHG CAG
scaffold1   2005    -   0   16  CHG CTG
scaffold1   2006    -   0   16  CHH CCT
scaffold1   2007    -   0   16  CHH CCC
scaffold1   2008    -   0   16  CHH CCC
scaffold1   2010    +   0   6   CHH CTC
scaffold1   2012    +   0   6   CHH CCA
scaffold1   2013    +   0   6   CHG CAG
scaffold1   2015    -   0   15  CHG CTG
scaffold1   2017    -   0   15  CHH CAC
scaffold1   2020    -   0   13  CHH CTT
scaffold1   2021    -   0   13  CHH CCT
scaffold1   2024    +   0   6   CHG CTG
scaffold1   2026    -   0   13  CHG CAG
scaffold1   2027    -   0   13  CHH CCA
scaffold1   2029    -   0   13  CHH CAC
scaffold1   2032    +   0   3   CHH CCT
scaffold1   2033    +   0   3   CHH CTC
scaffold1   2035    +   0   3   CHH CCA
scaffold1   2036    +   0   3   CHH CAT
scaffold1   2039    +   0   3   CHH CAT
scaffold1   2043    +   0   2   CHH CAA
scaffold1   2047    -   0   12  CHH CTT
scaffold1   2049    +   0   2   CHH CAT
scaffold1   2053    -   0   11  CHH CAA
scaffold1   2056    -   0   11  CHH CTA
scaffold1   2058    +   0   2   CHH CAA
scaffold1   2063    -   0   10  CHH CAA
scaffold1   2064    -   0   10  CHH CCA
scaffold1   2065    -   0   10  CHH CCC
scaffold1   2068    +   0   2   CHH CTT
scaffold1   2071    +   0   2   CHH CCA
scaffold1   2072    +   0   2   CHG CAG
scaffold1   2074    -   0   10  CHG CTG
scaffold1   2075    +   0   2   CHH CCT
scaffold1   2076    +   0   2   CHH CTT
scaffold1   2079    -   0   8   CHH CAA
scaffold1   2081    -   0   9   CHH CAC
scaffold1   2082    -   0   9   CHH CCA
scaffold1   2084    +   0   2   CHH CAC
scaffold1   2086    +   0   2   CHG CAG
scaffold1   2088    -   0   10  CHG CTG
scaffold1   2092    -   0   10  CHH CAA
scaffold1   2093    -   0   10  CHH CCA
scaffold1   2095    -   0   10  CHH CAC
scaffold1   2098    -   0   10  CHH CTT
scaffold1   2100    +   0   1   CHH CCC
scaffold1   2101    +   0   1   CHH CCT
scaffold1   2102    +   0   1   CHH CTT
scaffold1   2107    +   0   0   CHG CTG
scaffold1   2109    -   0   10  CHG CAG
scaffold1   2111    +   0   0   CHH CCC
scaffold1   2112    +   0   0   CHH CCC
scaffold1   2113    +   0   0   CHH CCC
scaffold1   2114    +   0   0   CHH CCC
scaffold1   2115    +   0   0   CHH CCC
scaffold1   2116    +   0   0   CHH CCA
scaffold1   2117    +   0   0   CHH CAT
scaffold1   2120    -   0   8   CHH CAT
scaffold1   2122    +   0   0   CHG CTG
scaffold1   2124    -   0   6   CHG CAG
scaffold1   2125    +   0   0   CHH CCC
scaffold1   2126    +   0   0   CHH CCC
scaffold1   2127    +   0   0   CHH CCC
scaffold1   2128    +   0   0   CHH CCT
scaffold1   2129    +   0   0   CHG CTG
scaffold1   2131    -   0   6   CHG CAG
scaffold1   2133    -   0   6   CHH CAC
scaffold1   2136    +   0   0   CHG CAG
scaffold1   2138    -   0   6   CHG CTG
scaffold1   2140    -   0   6   CHH CTC
scaffold1   2141    +   0   0   CHH CCA
scaffold1   2142    +   0   0   CHG CAG
scaffold1   2144    -   0   6   CHG CTG
scaffold1   2145    +   0   0   CHH CTC
scaffold1   2147    +   0   0   CHH CCA
scaffold1   2148    +   0   0   CHH CAT
scaffold1   2152    +   0   0   CHG CAG
scaffold1   2154    -   0   5   CHG CTG
scaffold1   2156    +   0   0   CHH CAT
scaffold1   2159    -   0   5   CHH CAT
scaffold1   2160    -   0   5   CHH CCA
scaffold1   2162    -   0   5   CHH CAC
scaffold1   2164    -   0   5   CHH CAC
scaffold1   2166    +   0   0   CHH CCA
scaffold1   2167    +   0   0   CHG CAG
scaffold1   2169    -   0   5   CHG CTG
scaffold1   2171    -   0   5   CHH CAC
scaffold1   2173    -   0   4   CHH CAC
scaffold1   2174    -   0   4   CHH CCA
scaffold1   2176    -   0   4   CHH CAC
scaffold1   2177    -   0   4   CHH CCA
scaffold1   2179    -   0   4   CHH CTC
scaffold1   2180    -   0   4   CHH CCT
scaffold1   2183    +   0   0   CHH CTC
scaffold1   2185    +   0   0   CG  CGA
scaffold1   2186    -   3   0   CG  CGA
scaffold1   2188    -   0   3   CHH CTC
scaffold1   2190    -   0   3   CHH CAC
scaffold1   2192    +   0   0   CHH CCT
scaffold1   2193    +   0   0   CHG CTG
scaffold1   2195    -   0   3   CHG CAG
scaffold1   2196    +   0   0   CHH CAC
scaffold1   2198    +   0   0   CHG CAG
scaffold1   2200    -   0   2   CHG CTG
scaffold1   2202    -   0   2   CHH CTC
scaffold1   2203    +   0   0   CHH CCC
scaffold1   2204    +   0   0   CHH CCT
scaffold1   2205    +   0   0   CHG CTG
scaffold1   2207    -   0   2   CHG CAG
scaffold1   2209    +   0   0   CHH CCT
scaffold1   2210    +   0   0   CHH CTC
scaffold1   2212    +   0   0   CHH CCA
scaffold1   2213    +   0   0   CHH CAC
scaffold1   2215    +   0   0   CHH CCC
scaffold1   2216    +   0   0   CHH CCT
scaffold1   2217    +   0   0   CHH CTA
scaffold1   2220    +   0   0   CHG CTG
scaffold1   2222    -   0   1   CHG CAG
scaffold1   2224    -   0   1   CHH CTC
scaffold1   2225    +   0   0   CHH CTC
scaffold1   2227    +   0   0   CHH CAA
scaffold1   2230    +   0   0   CHH CCC
scaffold1   2231    +   0   0   CHH CCT
scaffold1   2232    +   0   0   CHH CTA
scaffold1   2235    +   0   0   CHG CTG
scaffold1   2237    -   0   1   CHG CAG
scaffold1   2239    +   0   0   CHH CCT
scaffold1   2240    +   0   0   CHH CTC
scaffold1   2242    +   0   0   CHH CAA
scaffold1   2245    +   0   0   CHH CCC
scaffold1   2246    +   0   0   CHH CCT
scaffold1   2247    +   0   0   CHH CTA
scaffold1   2250    +   0   0   CHG CTG
scaffold1   2252    -   0   1   CHG CAG
scaffold1   2254    +   0   0   CHH CCT
scaffold1   2255    +   0   0   CHH CTC
scaffold1   2257    +   0   0   CHH CAC
scaffold1   2259    +   0   0   CHH CCC
scaffold1   2260    +   0   0   CHH CCT
scaffold1   2261    +   0   0   CHH CTA
scaffold1   2264    +   0   0   CHG CTG
scaffold1   2266    -   0   2   CHG CAG
scaffold1   2268    +   0   0   CHH CCT
scaffold1   2269    +   0   0   CHH CTC
scaffold1   2271    +   0   0   CHH CAC
scaffold1   2273    +   0   0   CHH CCC
scaffold1   2274    +   0   0   CHH CCT
scaffold1   2275    +   0   0   CHH CTA
scaffold1   2278    +   0   1   CHG CTG
scaffold1   2280    -   0   1   CHG CAG
scaffold1   2283    +   0   1   CHH CAC
scaffold1   2285    +   0   1   CHH CTT
scaffold1   2290    -   0   1   CHH CAA
scaffold1   2291    -   0   1   CHH CCA
scaffold1   2293    -   0   1   CHH CTC
scaffold1   2295    -   0   1   CHH CAC
scaffold1   2300    -   0   1   CHH CAA
scaffold1   2301    -   0   1   CHH CCA
scaffold1   2309    -   0   1   CHH CAA
scaffold1   2311    -   0   1   CHH CAC
scaffold1   2313    -   0   1   CHH CTC
scaffold1   2314    +   0   1   CHG CCG
scaffold1   2315    +   1   0   CG  CGG
scaffold1   2316    -   1   0   CG  CGG
scaffold1   2317    -   0   1   CHG CCG
scaffold1   2320    +   0   1   CHH CTT
scaffold1   2323    +   0   1   CHH CTC
scaffold1   2325    +   0   1   CHH CAT
scaffold1   2328    +   0   1   CHH CCC
scaffold1   2329    +   0   1   CHH CCA
scaffold1   2330    +   0   1   CHH CAA
scaffold1   2333    +   0   1   CHH CAT
scaffold1   2336    +   0   1   CHG CAG
scaffold1   2338    -   0   1   CHG CTG
scaffold1   2341    +   0   1   CHH CCT
scaffold1   2342    +   0   1   CHG CTG
scaffold1   2344    -   0   1   CHG CAG
scaffold1   2346    +   0   1   CHH CCT
scaffold1   2347    +   0   1   CHH CTC
scaffold1   2349    +   0   1   CHH CAC
scaffold1   2351    +   0   1   CHH CAA
scaffold1   2356    -   0   1   CHH CAT
scaffold1   2357    -   0   1   CHH CCA
scaffold1   2358    +   0   1   CHH CCA
scaffold1   2359    +   0   1   CHH CAC
scaffold1   2361    +   0   1   CHH CAA
scaffold1   2367    +   0   1   CHH CCC
scaffold1   2368    +   0   1   CHH CCA
scaffold1   2369    +   0   1   CHH CAC
scaffold1   2371    +   0   1   CHG CAG
scaffold1   2373    -   0   1   CHG CTG
scaffold1   2374    +   0   1   CHH CCA
scaffold1   2375    +   0   1   CHH CAC
scaffold1   2377    +   0   1   CHH CCC
scaffold1   2378    +   0   1   CHH CCT
scaffold1   2379    +   0   1   CHH CTC
scaffold1   2381    +   0   1   CHH CCT
scaffold1   2382    +   0   1   CHH CTA
scaffold1   2387    +   0   1   CHH CCC
scaffold1   2388    +   0   1   CHH CCC
scaffold1   2389    +   0   1   CHH CCC
scaffold1   2390    +   0   1   CHH CCC
scaffold1   2391    +   0   1   CHH CCA
scaffold1   2392    +   0   1   CHH CAA
scaffold1   2397    +   0   1   CHH CTT
scaffold1   2400    +   0   1   CHH CCC
scaffold1   2401    +   0   1   CHH CCA
scaffold1   2402    +   0   1   CHG CAG
scaffold1   2404    -   0   1   CHG CTG
scaffold1   2407    -   0   1   CHH CTT
scaffold1   2409    -   0   1   CHH CTC
scaffold1   2411    -   0   1   CHH CAC
scaffold1   2412    -   0   1   CHH CCA
scaffold1   2415    -   0   1   CHH CTT
scaffold1   2416    -   0   1   CHH CCT
scaffold1   2418    -   0   1   CHH CAC
scaffold1   2419    +   0   1   CHH CTA
scaffold1   2425    +   0   1   CHG CTG
scaffold1   2427    -   0   0   CHG CAG
scaffold1   2428    -   0   0   CHH CCA
scaffold1   2429    -   0   0   CHH CCC
scaffold1   2430    -   0   0   CHH CCC
scaffold1   2431    -   0   0   CHH CCC
scaffold1   2433    +   0   1   CHH CAA
scaffold1   2436    +   0   1   CHH CTC
scaffold1   2438    +   0   1   CHH CCA
scaffold1   2439    +   0   1   CHH CAT
scaffold1   2448    -   0   0   CHH CAT
scaffold1   2451    +   0   0   CG  CGA
scaffold1   2452    -   0   0   CG  CGT
scaffold1   2454    -   0   0   CHH CTC
scaffold1   2456    -   0   0   CHH CTC
scaffold1   2457    -   0   0   CHH CCT
scaffold1   2459    -   0   0   CHH CTC
scaffold1   2461    -   0   0   CHH CTC
scaffold1   2462    -   0   0   CHH CCT
scaffold1   2463    -   0   0   CHH CCC
scaffold1   2464    -   0   0   CHH CCC
scaffold1   2465    -   0   0   CHH CCC
scaffold1   2466    -   0   0   CHH CCC
scaffold1   2467    +   0   0   CHH CAA
scaffold1   2470    +   0   0   CHH CAA
scaffold1   2475    +   0   0   CHH CCA
scaffold1   2476    +   0   0   CHH CAT
scaffold1   2479    +   0   0   CG  CGT
scaffold1   2480    -   0   0   CG  CGA
scaffold1   2486    -   0   0   CHH CTA
scaffold1   2491    -   0   0   CHH CAT
scaffold1   2492    -   0   0   CHH CCA
scaffold1   2493    -   0   0   CHH CCC
scaffold1   2494    -   0   0   CHH CCC
scaffold1   2495    -   0   0   CHH CCC
scaffold1   2497    -   0   0   CHH CTC
scaffold1   2499    -   0   0   CHH CTC
scaffold1   2500    -   0   0   CHH CCT
scaffold1   2502    -   0   0   CHH CTC
scaffold1   2504    -   0   0   CHH CTC
scaffold1   2505    -   0   0   CHH CCT
scaffold1   2507    -   0   0   CHH CAC
scaffold1   2508    -   0   0   CHH CCA
scaffold1   2509    +   0   0   CHH CAA
scaffold1   2515    +   0   0   CHH CCA
scaffold1   2516    +   0   0   CHH CAT
scaffold1   2525    -   0   0   CHH CAT
scaffold1   2526    -   0   0   CHH CCA
scaffold1   2527    +   0   0   CHH CAA
scaffold1   2531    -   0   0   CHH CTT
scaffold1   2534    -   0   0   CHH CTT
scaffold1   2535    -   0   0   CHH CCT
scaffold1   2536    -   0   0   CHH CCC
scaffold1   2537    -   0   0   CHH CCC
scaffold1   2539    -   0   0   CHH CTC
scaffold1   2540    -   0   0   CHH CCT
scaffold1   2541    -   0   0   CHH CCC
scaffold1   2542    -   0   0   CHH CCC
scaffold1   2543    -   0   0   CHH CCC
scaffold1   2544    -   0   0   CHH CCC
scaffold1   2545    +   0   0   CHH CCN
scaffold1   2546    +   0   0   CHH CNT
scaffold1   2552    -   0   0   CHH CAT
scaffold1   2553    -   0   0   CHH CCA
scaffold1   2554    +   0   2   CHH CCA
scaffold1   2555    +   0   2   CHH CAT
scaffold1   2558    -   0   0   CHH CAT
scaffold1   2561    -   0   0   CHH CTT
scaffold1   2562    -   0   0   CHH CCT
scaffold1   2563    -   0   0   CHH CCC
scaffold1   2564    -   0   0   CHH CCC
scaffold1   2565    -   0   0   CHH CCC
scaffold1   2566    -   0   0   CHH CCC
scaffold1   2569    -   0   1   CHH CAA
scaffold1   2570    -   0   1   CHH CCA
scaffold1   2573    -   0   1   CHH CAT
scaffold1   2574    -   0   1   CHH CCA
scaffold1   2575    +   0   3   CHH CAA
scaffold1   2578    +   0   4   CHH CTC
scaffold1   2580    +   0   4   CHH CCA
scaffold1   2581    +   0   4   CHH CAT
scaffold1   2590    -   0   2   CHH CAT
scaffold1   2591    -   0   2   CHH CCA
scaffold1   2592    +   0   4   CHH CCA
scaffold1   2593    +   0   4   CHH CAT
scaffold1   2596    -   0   2   CHH CAT
scaffold1   2599    -   0   3   CHH CTT
scaffold1   2600    -   0   3   CHH CCT
scaffold1   2601    -   0   3   CHH CCC
scaffold1   2602    -   0   3   CHH CCC
scaffold1   2603    -   0   3   CHH CCC
scaffold1   2604    -   0   3   CHH CCC
scaffold1   2607    -   0   3   CHH CAA
scaffold1   2608    -   0   4   CHH CCA
scaffold1   2609    -   0   4   CHH CCC
scaffold1   2611    -   0   4   CHH CAC
scaffold1   2612    -   0   4   CHH CCA
scaffold1   2613    +   0   4   CHH CAA
scaffold1   2616    +   0   4   CHH CTC
scaffold1   2618    +   0   4   CHH CAA
scaffold1   2628    -   0   6   CHH CAT
scaffold1   2629    -   0   6   CHH CCA
scaffold1   2630    +   0   6   CHH CCA
scaffold1   2631    +   0   6   CHH CAT
scaffold1   2634    -   0   6   CHH CAT
scaffold1   2635    -   0   6   CHH CCA
scaffold1   2640    -   0   6   CHH CAA
scaffold1   2645    -   0   6   CHH CAT
scaffold1   2646    -   0   6   CHH CCA
scaffold1   2647    -   0   6   CHH CCC
scaffold1   2652    +   0   8   CHH CCA
scaffold1   2653    +   0   8   CHH CAT
scaffold1   2656    +   0   8   CHH CAA
scaffold1   2659    -   0   7   CHH CTT
scaffold1   2660    +   0   8   CHH CTC
scaffold1   2662    +   0   8   CHH CAC
scaffold1   2664    +   0   9   CHH CAT
scaffold1   2668    +   8   1   CG  CGA
scaffold1   2669    -   6   2   CG  CGT
scaffold1   2672    -   0   8   CHH CAT
scaffold1   2675    +   9   1   CG  CGG
scaffold1   2676    -   7   1   CG  CGA
scaffold1   2677    -   0   8   CHG CCG
scaffold1   2678    -   0   8   CHH CCC
scaffold1   2679    -   0   8   CHH CCC
scaffold1   2682    +   0   13  CHH CAC
scaffold1   2684    +   0   13  CHG CAG
scaffold1   2686    -   0   8   CHG CTG
scaffold1   2691    +   11  1   CG  CGG
scaffold1   2692    -   5   3   CG  CGA
scaffold1   2693    -   0   8   CHG CCG
scaffold1   2694    +   0   13  CHH CCA
scaffold1   2695    +   0   13  CHH CAC
scaffold1   2697    +   0   13  CHH CAT
scaffold1   2700    +   0   13  CHH CAC
scaffold1   2702    +   0   12  CHH CAT
scaffold1   2705    -   0   8   CHH CAT
scaffold1   2708    +   0   13  CHG CTG
scaffold1   2710    -   0   8   CHG CAG
scaffold1   2713    -   0   8   CHH CTT
scaffold1   2716    -   0   8   CHH CAA
scaffold1   2718    -   0   8   CHH CTC
scaffold1   2728    -   0   9   CHH CTT
scaffold1   2729    +   0   15  CHH CAA
scaffold1   2734    -   0   10  CHH CTA
scaffold1   2736    -   0   10  CHH CTC
scaffold1   2737    -   0   10  CHH CCT
scaffold1   2739    -   0   9   CHH CAC
scaffold1   2741    +   0   15  CHH CTA
scaffold1   2747    +   0   15  CHG CAG
scaffold1   2749    -   0   10  CHG CTG
scaffold1   2752    -   0   10  CHH CTT
scaffold1   2754    +   0   16  CHH CCC
scaffold1   2755    +   0   15  CHH CCA
scaffold1   2756    +   1   14  CHH CAC
scaffold1   2758    +   0   15  CHG CCG
scaffold1   2759    +   7   8   CG  CGG
scaffold1   2760    -   2   8   CG  CGG
scaffold1   2761    -   0   10  CHG CCG
scaffold1   2763    -   0   11  CHH CAC
scaffold1   2764    -   0   11  CHH CCA
scaffold1   2766    -   0   11  CHH CTC
scaffold1   2770    -   0   11  CHH CAT
scaffold1   2772    +   7   8   CG  CGT
scaffold1   2773    -   6   5   CG  CGT
scaffold1   2775    +   0   15  CHH CCT
scaffold1   2776    +   0   14  CHG CTG
scaffold1   2778    -   0   10  CHG CAG
scaffold1   2780    +   0   13  CHG CTG
scaffold1   2782    -   0   11  CHG CAG
scaffold1   2783    -   0   11  CHH CCA
scaffold1   2786    -   0   11  CHH CAA
scaffold1   2787    +   0   16  CHH CTA
scaffold1   2791    -   0   11  CHH CTT
scaffold1   2792    -   0   11  CHH CCT
scaffold1   2793    -   0   11  CHH CCC
scaffold1   2798    +   0   17  CHH CTT
scaffold1   2802    -   0   13  CHH CAA
scaffold1   2806    +   0   17  CHH CCT
scaffold1   2807    +   0   16  CHH CTT
scaffold1   2810    +   0   16  CHH CCA
scaffold1   2811    +   0   16  CHG CAG
scaffold1   2813    -   0   13  CHG CTG
scaffold1   2814    -   0   13  CHH CCT
scaffold1   2819    +   0   16  CHG CTG
scaffold1   2821    -   0   14  CHG CAG
scaffold1   2823    -   0   14  CHH CTC
scaffold1   2829    -   0   14  CHH CAT
scaffold1   2833    -   0   15  CHH CAA
scaffold1   2834    +   0   17  CHG CCG
scaffold1   2835    +   10  7   CG  CGA
scaffold1   2836    -   7   8   CG  CGG
scaffold1   2840    -   1   14  CHH CAA
scaffold1   2842    -   0   14  CHH CAC
scaffold1   2845    -   0   15  CHH CTT
scaffold1   2846    -   0   15  CHH CCT
scaffold1   2849    -   0   15  CHH CTT
scaffold1   2853    -   0   15  CHH CAA
scaffold1   2857    +   0   17  CHH CAA
scaffold1   2861    -   0   13  CHH CAT
scaffold1   2866    +   0   17  CHH CCC
scaffold1   2867    +   0   17  CHH CCC
scaffold1   2868    +   0   17  CHH CCA
scaffold1   2869    +   0   17  CHH CAT
scaffold1   2873    +   0   15  CHH CAA
scaffold1   2877    -   0   13  CHH CAT
scaffold1   2878    +   0   15  CHH CAC
scaffold1   2880    +   0   15  CHH CTC
scaffold1   2882    +   0   15  CHG CTG
scaffold1   2884    -   0   13  CHG CAG
scaffold1   2888    +   0   16  CHG CTG
scaffold1   2890    -   0   12  CHG CAG
scaffold1   2891    -   0   12  CHH CCA
scaffold1   2894    +   0   15  CHH CAC
scaffold1   2896    +   0   15  CHG CCG
scaffold1   2897    +   6   9   CG  CGA
scaffold1   2898    -   3   10  CG  CGG
scaffold1   2901    +   0   15  CHH CCC
scaffold1   2902    +   0   15  CHG CCG
scaffold1   2903    +   6   9   CG  CGG
scaffold1   2904    -   4   9   CG  CGG
scaffold1   2905    -   0   13  CHG CCG
scaffold1   2906    -   0   13  CHH CCC
scaffold1   2909    +   0   14  CHH CAC
scaffold1   2911    +   0   13  CHH CAT
scaffold1   2914    -   0   12  CHH CAT
scaffold1   2916    +   0   12  CHH CAT
scaffold1   2921    -   0   13  CHH CAT
scaffold1   2924    +   0   9   CHH CTA
scaffold1   2928    -   0   12  CHH CAT
scaffold1   2932    +   0   9   CHH CTT
scaffold1   2937    +   0   9   CHH CCA
scaffold1   2938    +   0   9   CHH CAT
scaffold1   2941    +   0   9   CHH CAC
scaffold1   2943    +   0   8   CHH CCA
scaffold1   2944    +   1   7   CHG CAG
scaffold1   2946    -   0   12  CHG CTG
scaffold1   2947    +   0   8   CHH CCA
scaffold1   2948    +   1   8   CHG CAG
scaffold1   2950    -   0   12  CHG CTG
scaffold1   2953    +   0   8   CHH CTT
scaffold1   2957    +   0   8   CHH CAA
scaffold1   2964    +   0   8   CHH CAA
scaffold1   2967    +   0   9   CHH CAA
scaffold1   2970    +   0   9   CHH CCT
scaffold1   2971    +   0   8   CHH CTC
scaffold1   2973    +   0   8   CHH CAA
scaffold1   2979    +   0   9   CHH CAT
scaffold1   2986    +   3   6   CG  CGT
scaffold1   2987    -   4   9   CG  CGT
scaffold1   2992    -   0   14  CHH CAA
scaffold1   2994    -   0   13  CHH CTC
scaffold1   2997    -   0   13  CHH CTT
scaffold1   3000    +   0   8   CHH CTC
scaffold1   3002    +   0   9   CHH CCT
scaffold1   3003    +   0   10  CHH CTC
scaffold1   3005    +   3   7   CG  CGT
scaffold1   3006    -   3   9   CG  CGA
scaffold1   3008    -   0   12  CHH CAC
scaffold1   3011    +   0   11  CHG CCG
scaffold1   3012    +   7   5   CG  CGG
scaffold1   3013    -   5   7   CG  CGG
scaffold1   3014    -   0   12  CHG CCG
scaffold1   3015    -   0   12  CHH CCC
scaffold1   3019    +   0   12  CHG CAG
scaffold1   3021    -   0   12  CHG CTG
scaffold1   3023    -   0   12  CHH CTC
scaffold1   3025    -   0   12  CHH CTC
scaffold1   3029    +   0   11  CHH CCT
scaffold1   3030    +   0   12  CHH CTA
scaffold1   3037    +   0   12  CHH CAA
scaffold1   3041    -   0   12  CHH CAT
scaffold1   3050    -   0   10  CHH CAT
scaffold1   3054    -   0   11  CHH CAA
scaffold1   3055    -   0   11  CHH CCA
scaffold1   3058    +   0   12  CHH CCC
scaffold1   3059    +   0   12  CHH CCT
scaffold1   3060    +   0   12  CHH CTC
scaffold1   3062    +   0   12  CHH CAT
scaffold1   3065    +   0   12  CHG CTG
scaffold1   3067    -   0   9   CHG CAG
scaffold1   3075    -   0   9   CHH CTT
scaffold1   3077    -   0   9   CHH CAC
scaffold1   3078    -   0   9   CHH CCA
scaffold1   3080    +   0   12  CHH CAT
scaffold1   3088    -   0   8   CHH CTT
scaffold1   3092    -   0   9   CHH CAA
scaffold1   3093    -   0   9   CHH CCA
scaffold1   3094    -   0   9   CHH CCC
scaffold1   3095    -   0   9   CHH CCC
scaffold1   3098    +   3   6   CG  CGC
scaffold1   3099    -   4   5   CG  CGA
scaffold1   3100    +   0   7   CHG CAG
scaffold1   3102    -   0   10  CHG CTG
scaffold1   3104    +   0   7   CHH CTC
scaffold1   3106    +   0   7   CHG CTG
scaffold1   3108    -   0   9   CHG CAG
scaffold1   3113    +   0   7   CHG CAG
scaffold1   3115    -   0   8   CHG CTG
scaffold1   3117    -   0   8   CHH CTC
scaffold1   3122    -   0   8   CHH CTT
scaffold1   3126    +   0   5   CHH CAT
scaffold1   3130    +   0   5   CHG CAG
scaffold1   3132    -   0   8   CHG CTG
scaffold1   3134    +   0   5   CHH CAC
scaffold1   3136    +   0   5   CHH CAT
scaffold1   3139    -   0   8   CHH CAT
scaffold1   3140    -   0   8   CHH CCA
scaffold1   3141    +   0   4   CHH CAC
scaffold1   3143    +   0   4   CHH CTC
scaffold1   3145    +   0   4   CHH CTC
scaffold1   3147    +   0   4   CHH CCC
scaffold1   3148    +   0   4   CHH CCT
scaffold1   3149    +   0   4   CHH CTC
scaffold1   3151    +   0   4   CHH CAC
scaffold1   3153    +   1   3   CG  CGT
scaffold1   3154    -   1   7   CG  CGT
scaffold1   3156    -   0   8   CHH CAC
scaffold1   3160    +   0   4   CHH CAC
scaffold1   3162    +   0   4   CHH CAC
scaffold1   3164    +   0   4   CHG CAG
scaffold1   3166    -   0   9   CHG CTG
scaffold1   3167    +   0   3   CHH CCC
scaffold1   3168    +   0   3   CHH CCC
scaffold1   3169    +   0   3   CHH CCA
scaffold1   3170    +   0   3   CHH CAT
scaffold1   3192    +   0   4   CHG CTG
scaffold1   3194    -   0   7   CHG CAG
scaffold1   3197    +   1   2   CHH CAT
scaffold1   3201    +   0   1   CHH CAC
scaffold1   3203    +   0   1   CHH CAC
scaffold1   3205    +   0   1   CHG CTG
scaffold1   3207    -   1   7   CHG CAG
scaffold1   3208    -   0   8   CHH CCA
scaffold1   3210    +   0   1   CHH CAC
scaffold1   3212    +   0   1   CHH CTT
scaffold1   3215    +   0   1   CHH CCT
scaffold1   3216    +   0   1   CHH CTC
scaffold1   3218    +   0   1   CHG CCG
scaffold1   3219    +   0   1   CG  CGG
scaffold1   3220    -   2   5   CG  CGG
scaffold1   3221    -   0   7   CHG CCG
scaffold1   3222    -   0   7   CHH CCC
scaffold1   3225    +   0   1   CHH CTC
scaffold1   3227    +   0   1   CG  CGG
scaffold1   3228    -   1   6   CG  CGA
scaffold1   3229    -   0   7   CHG CCG
scaffold1   3230    +   0   2   CG  CGC
scaffold1   3231    -   2   5   CG  CGC
scaffold1   3232    +   0   2   CHH CAC
scaffold1   3234    +   0   2   CHH CTC
scaffold1   3236    +   0   3   CHH CAC
scaffold1   3238    +   0   4   CHG CCG
scaffold1   3239    +   0   4   CG  CGT
scaffold1   3240    -   1   7   CG  CGG
scaffold1   3243    +   0   4   CG  CGA
scaffold1   3244    -   0   8   CG  CGT
scaffold1   3247    +   0   4   CHG CTG
scaffold1   3249    -   0   7   CHG CAG
scaffold1   3252    +   0   4   CHH CAT
scaffold1   3256    +   0   4   CHH CTC
scaffold1   3258    +   0   4   CHG CCG
scaffold1   3259    +   0   4   CG  CGC
scaffold1   3260    -   1   8   CG  CGG
scaffold1   3261    +   0   4   CG  CGT
scaffold1   3262    -   1   8   CG  CGC
scaffold1   3265    -   0   9   CHH CAA
scaffold1   3267    +   0   4   CG  CGT
scaffold1   3268    -   1   8   CG  CGA
scaffold1   3270    +   0   4   CHH CCT
scaffold1   3271    +   0   4   CHH CTC
scaffold1   3273    +   0   4   CG  CGG
scaffold1   3274    -   1   9   CG  CGA
scaffold1   3275    -   0   10  CHG CCG
scaffold1   3276    +   0   4   CHH CAT
scaffold1   3280    -   0   10  CHH CTA
scaffold1   3281    -   0   10  CHH CCT
scaffold1   3282    -   0   10  CHH CCC
scaffold1   3285    +   0   4   CHG CAG
scaffold1   3287    -   0   10  CHG CTG
scaffold1   3291    +   0   4   CHG CAG
scaffold1   3293    -   0   10  CHG CTG
scaffold1   3295    +   0   4   CHG CTG
scaffold1   3297    -   0   11  CHG CAG
scaffold1   3299    +   0   4   CHG CTG
scaffold1   3301    -   0   11  CHG CAG
scaffold1   3302    -   0   11  CHH CCA
scaffold1   3304    -   0   11  CHH CAC
scaffold1   3305    +   0   4   CHG CCG
scaffold1   3306    +   0   4   CG  CGG
scaffold1   3307    -   1   10  CG  CGG
scaffold1   3308    -   0   11  CHG CCG
scaffold1   3309    +   0   4   CHG CCG
scaffold1   3310    +   0   3   CG  CGC
scaffold1   3311    -   1   10  CG  CGG
scaffold1   3312    +   0   3   CG  CGC
scaffold1   3313    -   1   10  CG  CGC
scaffold1   3314    +   0   3   CG  CGC
scaffold1   3315    -   1   10  CG  CGC
scaffold1   3316    +   0   3   CHH CCC
scaffold1   3317    +   0   3   CHH CCC
scaffold1   3318    +   0   3   CHG CCG
scaffold1   3319    +   0   3   CG  CGT
scaffold1   3320    -   1   10  CG  CGG
scaffold1   3322    +   0   3   CHG CTG
scaffold1   3324    -   0   11  CHG CAG
scaffold1   3326    -   0   11  CHH CTC
scaffold1   3327    +   0   3   CG  CGC
scaffold1   3328    -   1   10  CG  CGC
scaffold1   3329    +   0   3   CHH CCT
scaffold1   3330    +   0   3   CHG CTG
scaffold1   3332    -   0   11  CHG CAG
scaffold1   3334    +   0   3   CHH CAC
scaffold1   3336    +   0   3   CHH CAC
scaffold1   3338    +   0   3   CG  CGC
scaffold1   3339    -   0   11  CG  CGT
scaffold1   3340    +   0   3   CHH CAC
scaffold1   3342    +   0   4   CHG CAG
scaffold1   3344    -   0   11  CHG CTG
scaffold1   3346    -   0   11  CHH CAC
scaffold1   3347    +   0   4   CHG CAG
scaffold1   3349    -   0   11  CHG CTG
scaffold1   3352    +   0   4   CHH CCT
scaffold1   3353    +   0   4   CHH CTC
scaffold1   3355    +   0   5   CHG CCG
scaffold1   3356    +   0   5   CG  CGC
scaffold1   3357    -   1   10  CG  CGG
scaffold1   3358    +   0   5   CHH CTC
scaffold1   3360    +   0   5   CG  CGC
scaffold1   3361    -   0   10  CG  CGA
scaffold1   3362    +   0   4   CHH CCC
scaffold1   3363    +   0   4   CHH CCC
scaffold1   3364    +   0   4   CHG CCG
scaffold1   3365    +   0   4   CG  CGT
scaffold1   3366    -   1   9   CG  CGG
scaffold1   3368    +   0   4   CHH CAC
scaffold1   3370    +   0   4   CHG CTG
scaffold1   3372    -   0   13  CHG CAG
scaffold1   3373    +   0   4   CHG CAG
scaffold1   3375    -   0   15  CHG CTG
scaffold1   3376    +   0   4   CHG CAG
scaffold1   3378    -   0   14  CHG CTG
scaffold1   3379    +   0   5   CHG CTG
scaffold1   3381    -   0   13  CHG CAG
scaffold1   3382    +   0   5   CHH CAT
scaffold1   3387    +   0   5   CHH CCT
scaffold1   3388    +   0   5   CHH CTT
scaffold1   3391    +   0   5   CHH CTT
scaffold1   3395    +   0   5   CHG CAG
scaffold1   3397    -   0   15  CHG CTG
scaffold1   3399    +   0   5   CHG CAG
scaffold1   3401    -   0   15  CHG CTG
scaffold1   3402    -   0   15  CHH CCT
scaffold1   3403    -   0   15  CHH CCC
scaffold1   3404    -   0   15  CHH CCC
scaffold1   3412    +   1   4   CG  CGT
scaffold1   3413    -   0   18  CG  CGA
scaffold1   3416    +   0   6   CHH CCA
scaffold1   3417    +   0   5   CHH CAT
scaffold1   3420    +   0   5   CHH CCC
scaffold1   3421    +   0   5   CHH CCT
scaffold1   3422    +   0   5   CHH CTC
scaffold1   3424    +   0   5   CHH CAC
scaffold1   3426    +   0   5   CHG CTG
scaffold1   3428    -   0   24  CHG CAG
scaffold1   3430    -   0   26  CHH CTC
scaffold1   3431    +   0   7   CHG CCG
scaffold1   3432    +   3   4   CG  CGA
scaffold1   3433    -   4   22  CG  CGG
scaffold1   3435    -   0   26  CHH CTC
scaffold1   3436    +   2   4   CG  CGC
scaffold1   3437    -   6   21  CG  CGC
scaffold1   3438    +   3   5   CG  CGA
scaffold1   3439    -   7   22  CG  CGC
scaffold1   3442    +   0   8   CHH CAT
scaffold1   3445    +   0   8   CHG CTG
scaffold1   3447    -   0   31  CHG CAG
scaffold1   3448    +   0   8   CHG CAG
scaffold1   3450    -   0   30  CHG CTG
scaffold1   3452    -   0   31  CHH CTC
scaffold1   3454    +   0   9   CHH CCC
scaffold1   3455    +   0   9   CHH CCA
scaffold1   3456    +   0   9   CHG CAG
scaffold1   3458    -   0   31  CHG CTG
scaffold1   3459    +   1   10  CHH CCA
scaffold1   3460    +   0   11  CHH CAC
scaffold1   3462    +   0   11  CHH CCC
scaffold1   3463    +   0   11  CHG CCG
scaffold1   3464    +   2   9   CG  CGA
scaffold1   3465    -   10  24  CG  CGG
scaffold1   3467    +   0   11  CHG CTG
scaffold1   3469    -   0   34  CHG CAG
scaffold1   3470    +   0   11  CHH CTC
scaffold1   3472    +   2   9   CG  CGT
scaffold1   3473    -   4   30  CG  CGA
scaffold1   3475    +   0   11  CHH CAC
scaffold1   3477    +   0   11  CHH CCC
scaffold1   3478    +   0   11  CHH CCT
scaffold1   3479    +   0   11  CHH CTA
scaffold1   3483    +   0   11  CHH CCC
scaffold1   3484    +   0   11  CHH CCT
scaffold1   3485    +   0   11  CHH CTA
scaffold1   3488    +   0   11  CHG CAG
scaffold1   3490    -   0   35  CHG CTG
scaffold1   3494    +   1   10  CG  CGT
scaffold1   3495    -   6   29  CG  CGT
scaffold1   3498    +   0   11  CHH CCA
scaffold1   3499    +   0   11  CHH CAT
scaffold1   3502    +   0   11  CHH CCC
scaffold1   3503    +   0   10  CHH CCT
scaffold1   3504    +   0   10  CHH CTC
scaffold1   3506    +   0   10  CHH CAC
scaffold1   3508    +   0   10  CHG CTG
scaffold1   3510    -   0   33  CHG CAG
scaffold1   3512    -   0   33  CHH CTC
scaffold1   3513    +   0   10  CHG CCG
scaffold1   3514    +   3   7   CG  CGA
scaffold1   3515    -   13  19  CG  CGG
scaffold1   3517    -   0   32  CHH CTC
scaffold1   3518    +   3   7   CG  CGC
scaffold1   3519    -   16  16  CG  CGC
scaffold1   3520    +   2   8   CG  CGA
scaffold1   3521    -   12  20  CG  CGC
scaffold1   3524    +   1   9   CHH CAT
scaffold1   3527    +   0   9   CHG CTG
scaffold1   3529    -   0   32  CHG CAG
scaffold1   3530    +   0   10  CHG CAG
scaffold1   3532    -   0   32  CHG CTG
scaffold1   3534    -   0   32  CHH CTC
scaffold1   3536    +   0   9   CHH CCC
scaffold1   3537    +   0   9   CHH CCA
scaffold1   3538    +   0   9   CHG CAG
scaffold1   3540    -   0   29  CHG CTG
scaffold1   3541    +   0   9   CHH CCA
scaffold1   3542    +   0   9   CHH CAC
scaffold1   3544    +   1   8   CHH CCC
scaffold1   3545    +   0   9   CHG CCG
scaffold1   3546    +   2   7   CG  CGA
scaffold1   3547    -   7   15  CG  CGG
scaffold1   3549    +   0   8   CHG CTG
scaffold1   3551    -   1   20  CHG CAG
scaffold1   3552    +   0   7   CHH CTC
scaffold1   3554    +   1   6   CG  CGT
scaffold1   3555    -   5   12  CG  CGA
scaffold1   3557    +   1   6   CHH CAC
scaffold1   3559    +   0   5   CHH CCC
scaffold1   3560    +   0   5   CHH CCT
scaffold1   3561    +   0   5   CHH CTA
scaffold1   3565    +   0   5   CHH CCC
scaffold1   3566    +   0   5   CHH CCT
scaffold1   3567    +   0   5   CHH CTA
scaffold1   3570    +   0   5   CHG CAG
scaffold1   3572    -   0   13  CHG CTG
scaffold1   3576    +   0   4   CHH CTT
scaffold1   3579    +   0   4   CHG CTG
scaffold1   3581    -   0   11  CHG CAG
scaffold1   3584    +   0   2   CHH CAA
scaffold1   3588    -   0   9   CHH CAT
scaffold1   3592    +   0   2   CHG CTG
scaffold1   3594    -   0   9   CHG CAG
scaffold1   3597    +   0   1   CHH CCC
scaffold1   3598    +   0   1   CHH CCC
scaffold1   3599    +   0   1   CHH CCA
scaffold1   3600    +   0   1   CHG CAG
scaffold1   3602    -   0   9   CHG CTG
scaffold1   3606    -   0   9   CHH CAT
scaffold1   3608    +   0   1   CHH CAA
scaffold1   3615    +   0   0   CG  CGC
scaffold1   3616    -   3   6   CG  CGA
scaffold1   3617    +   0   0   CHG CAG
scaffold1   3619    -   0   9   CHG CTG
scaffold1   3620    +   0   0   CHH CTT
scaffold1   3623    +   0   0   CHH CCA
scaffold1   3624    +   0   0   CHG CAG
scaffold1   3626    -   0   9   CHG CTG
scaffold1   3627    +   0   0   CHH CCC
scaffold1   3628    +   0   0   CHH CCT
scaffold1   3629    +   0   0   CHH CTT
scaffold1   3632    -   0   9   CHH CAA
scaffold1   3633    -   0   9   CHH CCA
scaffold1   3636    -   0   9   CHH CAT
scaffold1   3638    -   0   9   CHH CAC
scaffold1   3640    +   0   0   CHH CAT
scaffold1   3643    +   0   0   CHG CTG
scaffold1   3645    -   0   7   CHG CAG
scaffold1   3647    +   0   0   CHH CCC
scaffold1   3648    +   0   0   CHH CCC
scaffold1   3649    +   0   0   CHH CCT
scaffold1   3650    +   0   0   CHH CTC
scaffold1   3652    +   0   0   CHH CCC
scaffold1   3653    +   0   0   CHH CCC
scaffold1   3654    +   0   0   CHH CCC
scaffold1   3655    +   0   0   CHH CCC
scaffold1   3656    +   0   0   CHH CCA
scaffold1   3657    +   0   0   CHH CAT
scaffold1   3660    -   0   6   CHH CAT
scaffold1   3662    +   0   0   CHH CTT
scaffold1   3665    +   0   0   CHH CCC
scaffold1   3666    +   0   0   CHH CCA
scaffold1   3667    +   0   0   CHH CAT
scaffold1   3670    +   0   0   CHH CAN
scaffold1   4456    +   0   0   CHH CCC
scaffold1   4457    +   0   0   CHH CCC
scaffold1   4458    +   0   0   CHH CCT
scaffold1   4459    +   0   0   CHH CTA
scaffold1   4462    +   0   0   CHH CAA
scaffold1   4467    +   0   0   CHH CAA
scaffold1   4472    +   0   0   CHG CAG
scaffold1   4474    -   0   3   CHG CTG
scaffold1   4476    -   0   4   CHH CTC
scaffold1   4477    +   0   0   CHH CCC
scaffold1   4478    +   0   0   CHH CCC
scaffold1   4479    +   0   0   CHH CCC
scaffold1   4480    +   0   0   CHH CCT
scaffold1   4481    +   0   0   CHH CTC
scaffold1   4483    +   0   0   CHH CTC
scaffold1   4485    +   0   1   CHH CCT
scaffold1   4486    +   0   2   CHG CTG
scaffold1   4488    -   0   5   CHG CAG
scaffold1   4489    +   0   3   CHH CTT
scaffold1   4493    +   0   4   CHH CCT
scaffold1   4494    +   0   4   CHH CTT
scaffold1   4497    -   0   6   CHH CAA
scaffold1   4500    -   0   6   CHH CAA
scaffold1   4501    +   0   4   CHG CAG
scaffold1   4503    -   0   6   CHG CTG
scaffold1   4504    -   0   6   CHH CCT
scaffold1   4505    -   0   6   CHH CCC
scaffold1   4507    -   0   6   CHH CTC
scaffold1   4508    -   0   6   CHH CCT
scaffold1   4510    -   0   6   CHH CTC
scaffold1   4511    -   0   6   CHH CCT
scaffold1   4512    +   0   5   CHG CTG
scaffold1   4514    -   0   6   CHG CAG
scaffold1   4516    -   0   7   CHH CAC
scaffold1   4518    -   0   7   CHH CTC
scaffold1   4519    -   0   7   CHH CCT
scaffold1   4520    +   2   3   CG  CGG
scaffold1   4521    -   4   3   CG  CGC
scaffold1   4522    -   0   8   CHG CCG
scaffold1   4523    +   0   5   CHH CAC
scaffold1   4525    +   3   2   CG  CGT
scaffold1   4526    -   8   0   CG  CGT
scaffold1   4528    +   0   7   CHG CAG
scaffold1   4530    -   1   7   CHG CTG
scaffold1   4532    +   0   7   CHH CCC
scaffold1   4533    +   0   7   CHG CCG
scaffold1   4534    +   7   0   CG  CGG
scaffold1   4535    -   7   2   CG  CGG
scaffold1   4536    -   1   8   CHG CCG
scaffold1   4538    -   1   8   CHH CAC
scaffold1   4541    +   0   6   CHG CTG
scaffold1   4543    -   0   9   CHG CAG
scaffold1   4546    -   0   10  CHH CTA
scaffold1   4548    +   7   0   CG  CGA
scaffold1   4549    -   5   3   CG  CGA
scaffold1   4553    -   0   10  CHH CAA
scaffold1   4554    -   0   10  CHH CCA
scaffold1   4557    -   0   10  CHH CTA
scaffold1   4558    -   0   10  CHH CCT
scaffold1   4559    -   0   10  CHH CCC
scaffold1   4561    +   0   7   CHG CTG
scaffold1   4563    -   0   10  CHG CAG
scaffold1   4564    +   0   7   CHG CTG
scaffold1   4566    -   0   10  CHG CAG
scaffold1   4567    +   0   8   CHG CAG
scaffold1   4569    -   0   10  CHG CTG
scaffold1   4571    +   0   8   CHH CCT
scaffold1   4572    +   0   8   CHH CTT
scaffold1   4575    +   0   8   CHH CCC
scaffold1   4576    +   0   8   CHH CCA
scaffold1   4577    +   0   8   CHH CAA
scaffold1   4581    +   6   2   CG  CGA
scaffold1   4582    -   9   3   CG  CGA
scaffold1   4585    +   0   8   CHH CCT
scaffold1   4586    +   0   8   CHG CTG
scaffold1   4588    -   0   12  CHG CAG
scaffold1   4589    +   0   8   CHH CAC
scaffold1   4591    +   0   8   CHH CAA
scaffold1   4595    +   0   8   CHH CCT
scaffold1   4596    +   0   8   CHH CTT
scaffold1   4600    +   8   1   CG  CGG
scaffold1   4601    -   7   5   CG  CGA
scaffold1   4602    -   0   12  CHG CCG
scaffold1   4603    +   0   10  CHH CCA
scaffold1   4604    +   0   10  CHG CAG
scaffold1   4606    -   0   12  CHG CTG
scaffold1   4607    +   9   1   CG  CGT
scaffold1   4608    -   11  1   CG  CGC
scaffold1   4611    +   0   9   CHH CAC
scaffold1   4613    +   0   9   CHG CTG
scaffold1   4615    -   0   12  CHG CAG
scaffold1   4619    -   0   11  CHH CTT
scaffold1   4621    -   0   11  CHH CTC
scaffold1   4622    +   8   1   CG  CGC
scaffold1   4623    -   9   2   CG  CGC
scaffold1   4624    +   0   9   CHG CTG
scaffold1   4626    -   1   9   CHG CAG
scaffold1   4627    -   0   10  CHH CCA
scaffold1   4628    +   0   10  CHG CCG
scaffold1   4629    +   10  0   CG  CGA
scaffold1   4630    -   9   1   CG  CGG
scaffold1   4634    -   1   9   CHH CTT
scaffold1   4635    -   0   10  CHH CCT
scaffold1   4638    +   0   11  CHG CCG
scaffold1   4639    +   11  0   CG  CGG
scaffold1   4640    -   11  0   CG  CGG
scaffold1   4641    -   0   12  CHG CCG
scaffold1   4642    -   0   12  CHH CCC
scaffold1   4644    -   0   12  CHH CAC
scaffold1   4645    +   10  2   CG  CGG
scaffold1   4646    -   6   3   CG  CGC
scaffold1   4647    -   1   10  CHG CCG
scaffold1   4648    -   0   11  CHH CCC
scaffold1   4649    +   13  0   CG  CGC
scaffold1   4650    -   11  0   CG  CGC
scaffold1   4651    +   0   12  CHG CAG
scaffold1   4653    -   0   12  CHG CTG
scaffold1   4655    +   0   12  CHH CTC
scaffold1   4657    +   0   12  CHG CAG
scaffold1   4659    -   0   12  CHG CTG
scaffold1   4660    +   0   12  CHH CTA
scaffold1   4663    +   0   12  CHH CAC
scaffold1   4665    +   11  1   CG  CGG
scaffold1   4666    -   11  1   CG  CGT
scaffold1   4667    -   0   12  CHG CCG
scaffold1   4669    +   0   11  CHG CTG
scaffold1   4671    -   0   11  CHG CAG
scaffold1   4672    +   0   11  CHH CAT
scaffold1   4675    +   0   13  CHG CCG
scaffold1   4676    +   13  0   CG  CGA
scaffold1   4677    -   8   2   CG  CGG
scaffold1   4679    +   0   13  CHG CAG
scaffold1   4681    -   1   8   CHG CTG
scaffold1   4683    -   1   9   CHH CTC
scaffold1   4686    -   0   10  CHH CAT
scaffold1   4687    +   0   13  CHG CAG
scaffold1   4689    -   0   10  CHG CTG
scaffold1   4691    +   0   13  CHG CCG
scaffold1   4692    +   12  1   CG  CGT
scaffold1   4693    -   10  1   CG  CGG
scaffold1   4695    -   0   9   CHH CAC
scaffold1   4698    -   0   9   CHH CTA
scaffold1   4699    +   0   14  CHG CTG
scaffold1   4701    -   1   8   CHG CAG
scaffold1   4702    +   0   13  CHH CTC
scaffold1   4704    +   0   13  CHH CCC
scaffold1   4705    +   0   13  CHG CCG
scaffold1   4706    +   13  0   CG  CGC
scaffold1   4707    -   9   0   CG  CGG
scaffold1   4708    +   0   13  CHH CAA
scaffold1   4711    -   0   9   CHH CTT
scaffold1   4713    +   1   12  CHG CAG
scaffold1   4715    -   1   8   CHG CTG
scaffold1   4716    -   1   8   CHH CCT
scaffold1   4719    +   12  1   CG  CGA
scaffold1   4720    -   5   1   CG  CGT
scaffold1   4722    -   6   0   CHH CTC
scaffold1   4723    -   1   5   CHH CCT
scaffold1   4725    +   0   10  CHH CCT
scaffold1   4726    +   0   11  CHH CTT
scaffold1   4729    -   1   6   CHH CAA
scaffold1   4731    +   0   11  CHH CCA
scaffold1   4732    +   1   10  CHH CAC
scaffold1   4734    +   8   3   CG  CGT
scaffold1   4735    -   7   0   CG  CGT
scaffold1   4738    +   0   12  CHH CCT
scaffold1   4739    +   0   12  CHG CTG
scaffold1   4741    -   0   7   CHG CAG
scaffold1   4743    +   0   12  CHH CTT
scaffold1   4746    -   0   7   CHH CAA
scaffold1   4748    -   0   7   CHH CAC
scaffold1   4750    -   0   7   CHH CTC
scaffold1   4751    +   0   11  CHG CTG
scaffold1   4753    -   0   7   CHG CAG
scaffold1   4754    -   0   7   CHH CCA
scaffold1   4755    +   1   10  CHG CTG
scaffold1   4757    -   0   7   CHG CAG
scaffold1   4758    +   8   3   CG  CGG
scaffold1   4759    -   5   1   CG  CGC
scaffold1   4760    -   1   6   CHG CCG
scaffold1   4761    -   0   7   CHH CCC
scaffold1   4762    +   0   11  CHH CCA
scaffold1   4763    +   0   11  CHH CAC
scaffold1   4765    +   0   10  CHH CAA
scaffold1   4769    -   0   5   CHH CTT
scaffold1   4772    +   0   9   CHH CCA
scaffold1   4773    +   0   9   CHG CAG
scaffold1   4775    -   0   5   CHG CTG
scaffold1   4776    +   0   9   CHH CTC
scaffold1   4778    +   8   2   CG  CGC
scaffold1   4779    -   4   0   CG  CGA
scaffold1   4780    +   9   2   CG  CGG
scaffold1   4781    -   4   0   CG  CGC
scaffold1   4782    -   0   4   CHG CCG
scaffold1   4783    -   0   4   CHH CCC
scaffold1   4784    +   0   12  CHG CCG
scaffold1   4785    +   9   3   CG  CGC
scaffold1   4786    -   4   0   CG  CGG
scaffold1   4787    +   0   12  CHH CAA
scaffold1   4792    -   0   4   CHH CAA
scaffold1   4793    -   0   4   CHH CCA
scaffold1   4795    +   0   13  CHG CCG
scaffold1   4796    +   12  1   CG  CGC
scaffold1   4797    -   3   1   CG  CGG
scaffold1   4798    +   9   3   CG  CGG
scaffold1   4799    -   4   0   CG  CGC
scaffold1   4800    -   0   5   CHG CCG
scaffold1   4801    -   0   5   CHH CCC
scaffold1   4802    -   0   5   CHH CCC

This is my R-script:

library(bsseq)
list.files(pattern="*.txt") -> report.files
bsseq.data <-read.bismark(files=report.files,sampleNames=gsub(".txt","",report.files),rmZeroCov=TRUE,mc.cores=2, strandCollapse=FALSE,fileType="cytosineReport")

bsseq.data[[1]] <- c("low","low","low","low","high","high","high","high")
bsseq.data[[2]] <- c("pair1","pair2","pair3","pair4","pair1","pair2","pair3","pair4")
pData(bsseq.data) <- setNames(pData(bsseq.data),c("Type","pair"))

bsseq.data.smoothed <- BSmooth(bsseq.data, mc.cores=2, verbose=TRUE)
bsseq.data.smooth <- updateObject(bsseq.data.smoothed)

myBS.cov <- getCoverage(bsseq.data.smooth)

myLoci1<- which(rowSums(myBS.cov[,bsseq.data$Type == "high"] >= 2) >= 2 &rowSums(myBS.cov[, bsseq.data$Type == "low"] >= 2) >= 2)

bsseq.data.smooth1 <- bsseq.data.smooth[myLoci1,]

BSmooth.tstat(bsseq.data.smooth1,group1=c("LLiver_cytosine_report", "LZH369L_cytosine_report","LZH371L_cytosine_report","LZH373L_cytosine_report"),group2=c("MLS387L_cytosine_report", "MLS388L_cytosine_report","MLS390L_cytosine_report","MLS3L_cytosine_report"),estimate.var="group2",local.correct=TRUE, verbose=TRUE) -> bsseq.data.tstats1

#tcrit1 <- -qt(0.01/2, 10)

dmrs0 <- dmrFinder(bsseq.data.tstats1, cutoff = c(-4.6, 4.6),stat="tstat.corrected",verbose=TRUE)
dmrs <- subset(dmrs0, n >= 3 & abs(meanDiff) >= 0.1)
write.table(dmrs,file=Liver_DMR.txt,sep='\t',quote=FALSE)
PeteHaitch commented 6 years ago

Thanks for sharing. To confirm, can this error can be triggered with the first 2000 lines of the report that you shared?

PS. The rendering/formatting is Markdown which supported by lots of sites and frameworks - a very neat format. Some are even moving from LaTeX to Markdown for writing full scientific articles. In your case, you need to "fence" your code block with ``` on the lines before and after the code - if you're into LaTeX that corresponds to using \begin{verbatim} and \end{verbatim}. I've done that for your comments.

zyworship commented 6 years ago

@PeteHaitch Thank you so much, I don't be aware of this question. I try use Markdown to convert the frameworks.

PeteHaitch commented 6 years ago

@zyworship Are you able to trigger this error with the first 2000 lines of the report that you shared? Or only with the full files?

zyworship commented 6 years ago

maybe it can't trigger this error, only the full could trigger this.

发自网易邮箱大师 On 4/11/2018 23:05,Peter Hickeynotifications@github.com wrote:

@zyworship Are you able to trigger this error with the first 2000 lines of the report that you shared? Or only with the full files?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

PeteHaitch commented 6 years ago

Ok. I'll take a look with the example dataset, but without a reproducible example it's hard for me to know what might be the problem. Can you gzip one of the files and put it on Dropbox (or somewhere else)? It should be much smaller than 20 GB after gzipping it

PeteHaitch commented 6 years ago

To update: I'm unable to reproduce this with the example data. It's difficult for me to offer any more advice without a reproducible example.

zyworship commented 6 years ago

@PeteHaitch Thank you so much, I will try it again.