Error removing element

[jjfarrell]

One of our lumpy -pe runs aborted with an "Error removing element" message (see below). Any suggestions?

mean:252.3117 std:41.1445785385 309 0 1 1000000 2 1000000 3 1000000 4 1000000 5 1000000 6 1000000 7 1000000 8 1000000 9 1000000 10 1000000 11 1000000 12 1000000 13 1000000 13 2000000 13 4000000 13 8000000 13 16000000 13 32000000 14 1000000 14 2000000 14 4000000 14 8000000 14 16000000 14 32000000 15 1000000 15 2000000 15 4000000 15 8000000 15 16000000 15 32000000 16 1000000 17 1000000 18 1000000 19 1000000 20 1000000 21 1000000 21 2000000 21 4000000 21 8000000 21 16000000 Error removing element:21,46894658,46894610,+ 21,46894667,46894619,- 1 /var/spool/sge/scc-hd1/job_scripts/9025651: line 41: 23673 Aborted (core dumped) bin/lumpy -mw $WEIGHT -tt $TT -pe bam_file:$PE_BAM,histo_file:$OUT_DIR/$OUT_FILE.histo,m ean:$MEAN,stdev:$STDEV,read_length:$READ_LENGTH,min_non_overlap:$READ_LENGTH,discordant_z:4,back_distance:$BACK,weight:1,id:1,min_mapping_threshold:$MIN_MAP_T > $OUT_DIR/$OUT_FILE.pe.be dpe

[ryanlayer]

Can you email me a slice of that bam file? I think 20:46800000-46900000 will work.

[genecao]

got the same error on v0.2.6

[ryanlayer]

The "Error removing element" it typically the result of a strange alignment in the BAM. I keep the message/abort in the code so that I can continue to increase LUMPY's robustness. If you see this error, then please send me a slice of the BAM surrounding the coordinates reported in the error message. I can then account for that case in the code and provide a version of LUMPY that will work with your data.

[genecao]

could not find a email address to email, so I just paste details here:

Error removing element:chrA02,1059879,1060298,- chrA02,1060400,1060399,- 1 Aborted (core dumped)

bam slice attached in email

[ryanlayer]

I am having a little trouble parsing this when pasted into an email. Can you make a new bam file that contains these alignments (command below) and email them to me at rl6sf@virginia.edu?

samtools view -b sample.bam chrA02:1058000-1061000 > slice.bam

On Tue, Aug 26, 2014 at 2:54 PM, genecao notifications@github.com wrote:

here is the details:

Error removing element:chrA02,1059879,1060298,- chrA02,1060400,1060399,- 1 Aborted (core dumped)

bam slice:

HWI-ST1026:212:H0APPADXX:1:2206:1146:42729 163 chrA02 1059833 60 150M = 1060083 400 GCTTTGACGCCCTCTCCTGCACATTCTCTTGTGTGGTCTCCACTGGGTGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGT @@@DDD https://github.com/DDD?DFHHHH@GGGIIIIGHGIGGIGIIHIIIIGGHIIIGIII =BFHFIIIIIIIIIIIHFFFEEEEECCCBCDCCDCCCBBBBBBCBBBBBCCCCCBBCBBCCCCCB?CCBCCC@CA9BBCCCCBBBBB@4:?BBBBCBCCB? X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1110:9185:96275 83 chrA02 1059849 60 139M = 1059761 -227 CTGCACATTCTCTTGTGTGGTCTCCACTGGGTGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAG CCA:(:AA9BCB@@??1C8?@:??88CCB>44@C>A>>55<4C:@4 https://github.com/4 :A909@>?;9(9DFFFFHAD=EA@@AC https://github.com/AC@CGFB HWI-ST1026:212:H0APPADXX:2:2215:6410:81755 145 chrA02 1059853 37 148M = 1059857 -144 TCTTTCTCTTGTGTGGTCTCCACTGGGTGCTTCCCCCATGGACAAAGCTCTTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCTCAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCA ACCC?BCBBBBBA?@BCBCCCCBBBBCCBB3>(33:+:DCCCBB>9@BA88BB?CCCCCECEB?AA=CAEC@7 ;:IGIGIHF9B)FB?670)3:

*BB9 HWI-ST1026:212:H0APPADXX:2:2215:6410:81755 97 chrA02 1059857 37 146M = 1059853 144 TCTCTTGTGTGGTCTCCACTGGGTGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATG @@DDDDDHFCDHIDGBFHG4AAF+=B>?CCCCCBBCB?ACCCCBCCCBCCCCC@BBB>9ACBBBBB<((44:<?092>?ACB<?C?CCCCCCACABBBACC>C X0:i:1 X1:i:0 MD:Z:146 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1205:4838:65174 147 chrA02 1059869 60 150M = 1059829 -190 TCTCCACTGGGTGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTG CDDDCCDDBDDCDB@@BDBDDBCDDDCCADDDDDDEEDEDCC>BB@ BB@89<@BDCDDCADDFDDCC@CCCECCEDED@?DFBHHHEJIIIJIJIHJIIJJJJIFIJJJJJJJIIIIJJJJJIIIJJJJJJIJJJJIGHHHHHFFFFFCC@ X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2114:15536:39752 147 chrA02 1059871 60 150M = 1059753 -268 TCCACTGGGTGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTC CDCADDDDDDDDDDDDDDDDDDDDDDDDDDDDDEDDEDDDB>DDDDA@@ HWI-ST1026:212:H0APPADXX:2:2203:12594:32130 99 chrA02 1059880 60 151M = 1059953 223 TGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAG @CCFFFFFHHHHHJJJJJJJJJJIIIIJJJJJJIJJJJIJJJJIHIJJIIGGGHGFFFFCEEEDDDDDDDDDDDDBDDDDDDDDDDDDDDCC?BDDDDDDD?@BDDDDCDDDDDDDDDDDDDDEDDDDDDDBDDDEEEEDCBBDDDDDDDA X0:i:1 X1:i:0 MD:Z:151 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2106:4807:69648 83 chrA02 1059880 60 101M = 1059745 -236 TGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTC DDDDDDDDDDEDDDDDDDDDDDDDDDDEDDDDDDDFFHHJJIJJJIJJJJJJJJJIJIJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2106:13655:65622 147 chrA02 1059883 60 150M = 1059822 -211 TTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCG DBDDDDDEDDDDDDDDDDDDDCDDEDDDDBDDDDDDDDDDDDDDDDDEDDDEDDDDDDDDDEDCDDDDDDDDDDDDDDDEDFFFFHHHJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJIJJJJJJJJJJJIJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1107:8163:26118 163 chrA02 1059903 60 150M = 1060121 368 GTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAAT ?@@DFDDFHBFDDEEGIGHAG@FGGGCDDDGCDHIIIIIIIIIGEH@HH;=;6??.?;??1;ACEAC-;5;=BD(5(5:4:4@CD>ADBCACA@4:4@4>?<@8ACC@CCD@<CCDCCCCCCBBDD3?C X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2105:6134:61815 147 chrA02 1059903 60 100M = 1059856 -147 GTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGDECDEDDC@ HWI-ST1026:212:H0APPADXX:2:1111:19425:47528 163 chrA02 1059911 60 149M = 1059959 199 ATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCC @@@FFFFFHHHHGIIBHIGGHIIIJIJGGGIIIJJCDD@CB<@BBD https://github.com/BBD@BCCCAC>@BBBBD:@@:AC@? X0:i:1 X1:i:0 MD:Z:149 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2211:13918:86234 83 chrA02 1059921 60 100M = 1059753 -268 CCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTC DDDDDDDDDEDDDFDDDDDEEEEEEEFFFFFHHHHJJJJJJJJJJJIGJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2207:17872:75235 99 chrA02 1059922 60 101M = 1060047 225 CGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGT CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIIIDFBGFGIIIIIJJJEHHHHFDFFFFEEEDCDDDDDEDDDDDDDDDDDFEEEEDDB X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2108:4090:88101 99 chrA02 1059950 60 100M = 1060124 274 CAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAC@@FFFFFGCAFH;GFBGDHECGFHGHCE?DGHHGIGIGCEII@GCFGFIDBDCFI@CFHIJJDAHCHHF?BBCCCCACCD;?BBCCBCCCCCCDDDB X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2203:12594:32130 147 chrA02 1059953 60 150M = 1059880 -223 GCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAG CDDDDDDDDCCDDDDDDDDDDDDDDDDDDDDDDEDEDDDDDCDDDDDDCDDDDDDDEEEDDCCDDDB@??DCDDDDBDDEFFHHHGGJJJIHIJJJJJJIGB?HHJJJIJJJJJIGIIJJJIJJIJIIGJJIJJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:1105:7417:16977 147 chrA02 1059958 60 99M = 1059782 -275 GGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACDDDBCCDDCDDDDDDDDDDB@8CDDDCDDECECDDDEE@ CDDDCDDECECDDDEE@DD>HFHHCIGIGIHHEIGBF@FCIICGGEIHEIIIHFGCEGFFCGFGHHAHDDDDD=? X0:i:1 X1:i:0 MD:Z:99 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1111:19425:47528 83 chrA02 1059959 60 151M = 1059911 -199 GCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTG DBBCADDDDDDDDDDDCBDDDDDDDCCCCEDDDDCDCCCDDCDCCC@8>CDC@EDDDDBDDDDDBCCC=DDDDDC?ECCDFFFEEAJJIGF:CJIHFIIJJIIIJJJJJJJJIEJIIIIGIFIIIJIJJJIJJIIJJGHHHHHDDFFD@@@ X0:i:1 X1:i:0 MD:Z:151 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1212:10882:7753 99 chrA02 1059962 60 150M = 1060081 269 CACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAA CCCFFFDECFFHHGIJJIIICGHIJIGHHIIJIIJIIIJJIGHIIHJJJJJJJIJJGHIIJJJJJJJJIHHHFFFEEEEEECDC:BDDDDDDDDEDDCDDCCCDDEDDDCD>B5?BDDDCCDDDDDDCCCDDDDBBB?CDCACCDDDDDD X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2112:14859:31299 99 chrA02 1059964 60 101M = 1060070 206 CAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATT BCCFDFDEHHHHHJJJJJHIJJIJHHIJJJJJJJJJJJJHIJIJJJJJJJJJJIJIJJIJJJJJJJJJHHHFFFFEEEEEEDDDDDDDDDEEEEDDDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2216:14849:21575 83 chrA02 1059969 60 101M = 1059821 -249 GTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTAT DDDDDDDDDDDDDDDDDEDEDDDDDDDDDDDDEEEEDEFFFFFHHHFHHIHHHCHGJJJJIHIJIJJJJJJJJJJJJJJJJJJJIHFHHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1114:5974:67557 83 chrA02 1059970 60 101M = 1059693 -378 TGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATG ?DDDDDDDDDDDDDDDEDEDCDDDDDDDDDDDEEEEEDFFFFFFHHHHJJIIGIGJIJJJJIJIJJIJIIIIJJIJJJJJJJHHGCIHHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2108:7810:70230 163 chrA02 1059972 60 100M = 1060052 181 TGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATGCCCCFFFFEHHHHFIIJHHIJJJJJJJJJJJJIIJJJJJJJIGIJJJJJJJJJJIJJJJJIJAHIJFJHHHHHFDFFDDDDDDFEEEDDDDDDDDDEDDDD X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1202:16645:71758 163 chrA02 1059974 60 100M = 1060123 250 GGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATGCAG CC@FFDBDCFDFFHHFHGIJJIIJIJIJJGGGGGHIJJIIGIGIJIIFGIIIIGIIJJJGHGGIEHHEHEEHFFDDDDDDEEEECDDDCCDDCEDDDDED X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:1213:4941:40373 163 chrA02 1059991 60 100M = 1060057 167 AAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGACCCFFFFFHHHHHJJJJJJJJJJJJJJJHIJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJHHHHHHFFFFFFEEEEEEEDEDDDDDDDDDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2107:19287:55791 163 chrA02 1059991 60 100M = 1060057 167 AAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGA CCCFFFFFHHHHFIIJJJJJJJIJJJJJIHJJJJIJJJJJIJHGIJJJJIJIJJJJJJJJJHHHFHHFFFFFFEEDEEEEDEDDDDDDDDCDDDDDCDDD X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2208:5803:45833 83 chrA02 1060005 60 151M = 1059787 -369 GACAAAAATATCTGTCGTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATT CA9C@DDACCCBBBBBBCBCCCB@BBBBB@?CC>CABBB@ B@C@@CDB https://github.com/CDB>9:BCCDCC@CCCCCCCB@CCCBCCCCC?A?CCCCCB DD65WKN1:82:H0KAMADXX:1:2208:8732:58355 163 chrA02 1060021 60 100M = 1060263 343 GTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTC@@FFFFFHHHGHIIJJJJJJJJJJJJJIJJJIJJJIIJJJIIIIJJJIJJJJJJJJIJJJHHHHHHFFFFFFEDCDDDDEDDDDDDDDDDDEDDDDDDC X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2205:15799:94412 163 chrA02 1060021 60 100M = 1060156 236 GTCTCCATAGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGT @C@FFFFFHGHHFIIJIGIJIGIHGIJIJJJJGJJIJIIJIGHJJJIIJIJIJJJIIJIJJHHHHGGFFFFFFEDABDBDDDACCDDDCCCDEDDDDCC@ X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:2207:7844:91666 163 chrA02 1060029 60 145M = 1060150 272 AGCGTCCCAGCTCTGACGCCAAATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAG CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJJJJJJJJJJIJJIIJIIIJJJIJGJIGIIIIHHHBFFDEEEEEEDDDDDDDEDDDDDD@DDDDDDDDDDBDDDDDDDDDDDDDDD8ACDDDDDDDDDDDDDEDEEDDDDDDD X0:i:1 X1:i:0 MD:Z:145 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2211:9816:48412 147 chrA02 1060036 60 100M = 1059672 -464 CAGCTCTGACGCCAAATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACDDDDCDDDDDDDDDFEFDDCDCDEEEEEFFFFFFHHHHHJJIIJIJHIIGJJJJJIJJJJIIJIIGIIJJJJJJJJJIJJJJJJJJIGHHHHFFFFF@@@ X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:23 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2207:17872:75235 147 chrA02 1060047 60 100M = 1059922 -225 CCAAATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGG DCEEEEDCCDDDEDDDDDDDDDDDDDDDDDEEEFFFFHHHHHHJJJJJJJJJJJIHIJJIJJIJJJJJJIJJJJJJJJJIGHIIJJIHGHHHFFFFF@@@ X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:2113:4060:30466 81 chrA02 1060050 37 149M = 1060052 -147 CTTATACTCCAGCTTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAG BAB>3(1894:9(>:3>:@?8+4@>::>:9?A;;;:B@;;;5=5'1;;?;,,)=..(--58)=<==ADDDAFFG?90 DD65WKN1:82:H0KAMADXX:1:2111:18347:14974 163 chrA02 1060051 60 100M = 1060263 313 ATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAG CCCFFFFFHHHHHJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHIIJJJIJJJJJJJJIJGHJHHHFFFFEDDEDDDDDDDDDDCDD8CCD X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2214:12466:18853 163 chrA02 1060051 60 100M = 1060263 313 ATATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAG @CCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJJJJJJIIJJJJJJIIDHIIIJJIJJIGIJJJJIJJJIJJHGHFFFFEDDEDDDDDDDDDDC@B DD65WKN1:82:H0KAMADXX:2:2114:11286:91618 99 chrA02 1060052 60 101M = 1060099 147 TATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCC CCCFFFFFGHHHHJJJJIJJJJJJJJIIJJJJJJIJJJJJIHIJGIIJJGIIHIGJIJIIJJJJJIJJJIJHHHHFFEEDBEDDDDDDD?CDCBD?CCDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2201:8181:61321 163 chrA02 1060052 60 100M = 1060125 174 TATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJJJJJJJEIIIIIHIJIHGIIJJJJJJIIJJJJJJJJHIJHHHHFFFEDDEDDDDDDDDDDCBD8ACDD X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:2113:4060:30466 161 chrA02 1060052 37 140M = 1060050 147 TATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAG ?@?DD;ADFDABFFB8C<@C???C DD65WKN1:82:H0KAMADXX:2:2108:7810:70230 83 chrA02 1060052 60 101M = 1059972 -181 TATACTCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCC CDDDDDDEDDDDDDDDDDDDDDDDDDDDEEEEEFFFFFFHHJJJJJIJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJJIJIJIJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:1213:4941:40373 83 chrA02 1060057 60 101M = 1059991 -167 TCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGT ADEDDDDDDDDDDDDDDDDDDDDDDDDDEEEEEDFFHHHJJJJJJJIJJIJJJJJJJJJJJJJJJJJJJJHGJJJIIHJJJJJJJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2107:19287:55791 83 chrA02 1060057 60 101M = 1059991 -167 TCCAGATTCTTATGCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGT CDEDDDDDDDDDDDDDDDDDDDDDDDDDEEEEEDFFHHHJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJIGJJJJHHJJIJJJJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2112:14859:31299 147 chrA02 1060070 60 100M = 1059964 -206 GCAGGGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCC DDDDDDDDDDDDCDDDDDDDDDDDDEEFFFFFHHHHJJJJJJIJJJJJJJJJJJJJIHFJJJIGFJIJJJJJJJJJJIJJJJJJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:1116:2037:40290 99 chrA02 1060074 60 101M = 1060225 250 GGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGG CCCFFFFFHHHHHIIJBHGHHIHIICGFHIJJIJIJGHJIJIIIJIHIJJCHGIJIJJJJJJJHIHHEHFCDD=ACCCDDDDDEDDCDDDDEEDDDDDDCD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1104:2257:41848 163 chrA02 1060074 60 148M = 1060180 251 GGCAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTA @CCFFFFFHHHHGJJJJJJJJJFHIGGIIGHIJJIJIJJJJIJIJJHIJJIIJJJJJJIJJJJJIHHEHF?DC;@CEDDDDDDDDDCDDEDDEDCDDCCDACCDDDCDCDDDDD:ACCAACBBDD X0:i:1 X1:i:0 MD:Z:148 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2210:12752:99224 147 chrA02 1060076 60 148M = 1059798 -426 CAAGCTCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAG ?:CCACC?CCA>CCCCCCBCCCCCCCB@BCCCCDDCAECCCCBCB HWI-ST1026:212:H0APPADXX:2:1212:10882:7753 147 chrA02 1060081 60 150M = 1059962 -269 TCTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATG C@DDCCDDDDBBB?DDDDDDDDDDCDCDCCDDDDDCADDDDBB@:BDDA?5,BCCDDCCADDCCC@>AEA;DFFFHFEHEHAG@CC73HAIHHBGIJIHGHCFGHJJIJIIGGIJIIIHHEGIGAFHFFGHGIIGHHDHFDDDAD@@@ X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1213:6237:12378 163 chrA02 1060082 60 100M = 1060108 127 CTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATC@CFFFFFHHHHHJGIJGGIIEHIJJJJJJIJJJIJIIIJJIJJJJJIJJIIJJJJJJIJJJIHH?CEFFFFDEEEEEDDDEDDDDDDDDDCDDDDDDDE X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2107:7550:65512 99 chrA02 1060082 60 147M = 1060278 344 CTTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACA @@@FFFFFHGHHHGHBHBGHBHHIGF@FGGGIJCCBHIIJJIEDEGEHGIJJJIE6@=C3@@=CBHFFDCEFEEEEDEDDCDCEEACDDDD?CDBCDDDEDCBDDDDDDC>CCDCCD@CA>A@>@ACAACA@CC9:>?9A?:A+9A?X0:i:1 X1:i:0 MD:Z:147 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:2206:1146:42729 83 chrA02 1060083 60 150M = 1059833 -400 TTTCTTGAGCTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTT C?DDCCC<>BDBCCDDAC>8DDCCC@DEDDECCCDDDDDBDDDB9DCDDDBDDDDDDDDDDDDDDDCDDCCB@CDFFHHHHGHJIGJIIGAIEHFCCF9JJIGJIJGJIDJJJJJGIJJHFG 9DCDDDBDDDDDDDDDDDDDDDCDDCCB@CDFFHHHHGHJIGJIIGAIEHFCCF9JJIGJIJGJIDJJJJJGIJJHFGIIGIHIGHBHIGJHHHHGDDFFFCCC X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1107:7944:35767 99 chrA02 1060092 60 101M = 1060196 204 CTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGT CCCFFFFDHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJIJJJJJJJJIHIHHHBFHIJJIJHHHHHHFFFFFFEEEEDEDDDBDDDDFED9ABDDDDDC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2108:16516:46301 99 chrA02 1060092 60 101M = 1060196 204 CTCGTAGTGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGT CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFGIJJJJJHHHHHHFFFFFFCEEEEEDDDDDDDDFEDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2114:11286:91618 147 chrA02 1060099 60 100M = 1060052 -147 TGAGTCCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAG DDDDDDDDDEEEDDEDDDDBDDDC=FFFB?HFHJJIJJJIGIHJJJJJJIGHJIHIIHGIJIFJJJJJJIJJJJJJIJJJJJIJIJJHHHHHFFFFFCBC X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1105:18844:34441 99 chrA02 1060104 60 101M = 1060208 204 CCTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAA CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJFHJHHHBGIJJJJHJIJJJGHJJJJJHIHHHHHFFFFDDEEEEDDDDDDDDDEDEDDDDDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1113:12264:49780 99 chrA02 1060105 60 101M = 1060205 200 CTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAAC CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJHIJ?FHJJJIJJIIJJJIJJJJJHIJHHHHHFFFFEEEEEDDDDDDDDCDDEDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1116:19564:59075 99 chrA02 1060105 60 101M = 1060205 200 CTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAAC CCCFFFFFHHHHHJJIJJIJJJJJJJJJJJJJJJJJJJIIIJ?DHIJJIJJJJJJJJJJJJJIJJHHHHHFFFFEEEEEDDDDCDDDCDDDDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2103:11098:16547 163 chrA02 1060105 60 100M = 1060204 200 CTCTGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAA @@@FFFFFHHGHFJGFGCCFGFHFFGGEHIIJHIIIHIIBDGFI>@;CCCCA@C X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1213:6237:12378 83 chrA02 1060108 60 101M = 1060082 -127 TGAATAAGCATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCC EEEDDEDDDDDDDDDDDDBA;EFFFFFHJIIJJJJJJJJJJJJIIIJJJIHJJIIJIJJJIJIJJJJJIJJJIJJJIHEIJJJJJJJJHHHHHFFDDFCB@ X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1215:5919:50052 99 chrA02 1060117 60 150M = 1060173 206 ATGTTTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAG @@@DDFF https://github.com/DDFF>FFFDFHIIIIIIGGGIAHCDHGCHGFHIICGHGHIIHGGIEHIGIIIIBGEACHHHFGCEFFFC@C6(;AB;A@@CDCCCACAC>>ACCACC358<?BCC39ACC@CDCDCCBCDCACCACCACD CC@CDCDCCBCDCACCACCACD?CCCD?ACC?BDDDD X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1107:8163:26118 83 chrA02 1060121 60 150M = 1059903 -368 TTTCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATAC BAB:ADDDDCC>DDCDDDEDDDDDDA DD65WKN1:82:H0KAMADXX:1:1202:16645:71758 83 chrA02 1060123 60 101M = 1059974 -250 TCGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAG DBDDBCDDDDBBDDCDDDEDECEEFFDFGHGHHIJIJJJJIJJIIIIGJIIJIGJJJJJIHGIJJJJIJIGHIJJJJIJIHHJJIGJHHGHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2108:4090:88101 147 chrA02 1060124 60 100M = 1059950 -274 CGAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGBAAEDECEEDFD@?=AECCHDCGC>GGHIHIIGGHFGGIIIIGIGHE>BIIGJJJJIIHIHGCHFGHIGGCIIFHFHFBBDD?@@@ X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1215:9471:92284 163 chrA02 1060125 60 100M = 1060565 541 GAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGC@@@FFFFFHHHHHJJJFIJEIJCGIIJIJIJJJJJIJJJJJIIJIIJJIIIIJIJJJIJJJJJJHHFHHHFFFFFFEEEEEDDDDDDDDCDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2201:8181:61321 83 chrA02 1060125 60 101M = 1060052 -174 GAAACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCC CDB>DDDDDBDDDDDDDDEEEEEFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJIJJIJJJJIJJJJIJJJJJJJJJJIJJJJJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2113:16946:26277 99 chrA02 1060128 60 151M = 1060203 225 ACCCATACGCCTGAGGAGGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCAC CCCFFFFFHHHHHGIIGHIAFHIJJJJJJIIIIJJJJJJIJJJJJJJJJJJIIJIJJJJJJJJJDHHHHHHHFFFFFFEEEEEECDACCDDDDDDCCDDDDDDEEEDDDDDDDDDDEDDEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD? X0:i:1 X1:i:0 MD:Z:151 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2212:6899:2989 99 chrA02 1060145 60 101M = 1060290 243 GGTAAGCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATC @@@FFFFFGHHHFHGJIGIIIIDHIGIJJJIIHIJIIIIIIIJIIGHGIGGIJIJJJIJJGEGIJJGGGDHHIIHHHFFFFFEEEEEEEDDDDDDCDDDED X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:2207:7844:91666 83 chrA02 1060150 60 151M = 1060029 -272 GCCATTGTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATAT ?DDDDDDDDEEEEDDDCDDDDDDDDDEDDDDDDDDDDDDDDDDDDDDDCCDEDDDDDDCDDDDDDDDDEFFFFEEEAHHJJIIJJJJIJIIIIJIJJJJIIJIIJJIHJJJJJJJIJJHFGJIHIJGGJJIJJIJIIJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:151 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2205:15799:94412 83 chrA02 1060156 60 101M = 1060021 -236 GTTGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAG DDDEEEEDDDDDDDDDDDDDEDDDDDDEDEFFFFFFHHHHHJJJJJJIHIGIJJJIJJJIHJJJJJJJJIIJJJJJJJJJHGIJJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2205:13850:98755 99 chrA02 1060158 60 101M = 1060292 234 TGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGAC CCCFFFFFHGHHHJIIIIIJIJJJJJJJJJJIIIIJJJJJJJJJIJJJHIJJIJHIHIJJJIJJJIJJJJHGHGHGFFFFFEEDEEEDDEDDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2114:6186:83181 99 chrA02 1060158 60 101M = 1060292 234 TGATGAATAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGAC CCCFFFFFHHHHHJJJJJJJJJJJJJIJJJJJJJIIJJJIJIJJIJJJJJJJJJJJHIIIJHIJJJJJJIHHHHHHFFFFFEEEEEEDDEDDDDDDDDDDA X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1201:17783:76776 99 chrA02 1060165 60 150M = 1060276 261 TAGCCAAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAA BC?DFFFFFHGHHJJJJJJIIJJIFIIHHHGCHIIIHGGIIIEGIIJJJHIIIIIJJJEGGEIJJJGGJJGHHHFFFFFFCECEEEDDDCDDDDDDDDDDDDCCDDCDCCBDDDDD@BBDCCCCDCDCCCDDCDEDED@CBDDDDDDBCD X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2105:12531:92650 97 chrA02 1060170 37 137M = 1060170 137 AAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTA @@CDFFDBFHFHHIGIBGHIBFDBHCHHEFEH9CGDGBDDHFGG?9BFHHGIIFEDHIIGI;@CHDHCHHBEEHE@C;;?CEEEECC??;AABACDDA>>@>:>C1CDC X0:i:1 X1:i:0 MD:Z:137 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2105:12531:92650 145 chrA02 1060170 37 137M = 1060170 -137 AAAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTA CDCDC>::3CC?BD?CAADCCCCCCDDDDDCDCC@<:>>DC; HWI-ST1026:212:H0APPADXX:1:1113:12987:5489 97 chrA02 1060171 37 105M = 1060171 105 AAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAG @@?EFB+91@EEFIII>?B?DFEEBDDFFFFEI9CBFFCFGCA@DEE?ECEFEDDB7;@CA https://github.com/CA>BBBBB@BBBBBB:>@A https://github.com/A@<@ X0:i:1 X1:i:0 MD:Z:105 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1113:12987:5489 145 chrA02 1060171 37 105M = 1060171 -105 AAGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAG DDCCA@@CDCDDBDDDDCCC?;5A>CCEECECCDFDD?EGHFHGF7HFB>GFD???B@BGDGGHGCBGFCEC DD65WKN1:82:H0KAMADXX:1:1115:16779:37508 163 chrA02 1060172 60 100M = 1060318 247 AGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACA CCCFFFFFHHHHHJJJJJJJIJIHIIJJIJJJJJJJJJJJIJCHHHJJJJJJJJJJJJJIJJJJJJJJJJIHHHHHHFFFFFEEEEEDDDDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1207:12415:36278 99 chrA02 1060172 60 150M = 1060269 247 AGGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAAC CCCFFFFFHHHHHJJJJJJJIJIJJJJJJJJJJJJJIJIJJJHIJJIJJJJJJJJJJJJHIGJJJIJJJJJHHHHHHFFFFFEEEEEDDCDDDDDDDDDDDCDDDDDDDDDDDDDDDDDDDDDDDDDEEED>ABDDDDDDDDDDDDDDCD X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1215:5919:50052 147 chrA02 1060173 60 150M = 1060117 -206 GGGATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACT CC>C@DCD@??B@>C@DDCDCCC@CADCDCA:CDDDDCDDBBB?@DCCAA9:3;DCA?;@BA https://github.com/BA=69DDFCCEACHA4AAGECGCF;GCIGFIHGDB8G@=GFBIIHDD@@FCHAJIJIJJJJGIHEJJIFDFHFEFFFD?@@ X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1105:6235:32755 99 chrA02 1060176 60 151M = 1060373 347 ATCTATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTG @CCFFFFFHHHHGIJGEHGJIIJJJJJJJIIJIJFJIJJJIIJIIIIJIJJIEHIIHIIIJGIJIGJJJJIGGHHHHFFFFFEEDEDDCDDDDDDDDDDDD:5?CDBDDCCCDDDDDDDDDDDEEEDAABCC?BBDDDDCCCADABDCCDC X0:i:1 X1:i:0 MD:Z:151 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1104:2257:41848 83 chrA02 1060180 60 145M = 1060074 -251 ATGGCCCATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCT

BAJHFIIIHIIIGJJJIIGHGIIIIIIJJIJJIIJIFHFFHDDDDF@@? X0:i:1 X1:i:0 MD:Z:145 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1214:16561:14629 99 chrA02 1060187 60 101M = 1060386 299 ATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTAC CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFFFEEEEEEDDDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2110:4171:41120 99 chrA02 1060187 60 150M = 1060368 331 ATGAGTTCTTAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGAAACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCCTGGAAGAAACTT CCCFFFFFHHFHHJIJJJJJJJHIIJJIIIGIJJJIJJJJJJJJIIIIJJJIJIIIJIIIIJJJJJJJIIJJHHHHHFFFDCDEEDEDDDDDCDDDDDCDDCCDDDDDDDDDEDCDCCBDDDBDDDDDCDDACDDDD:@CCDDDDDDDDD X0:i:1 X1:i:0 MD:Z:81T55T12 RG:Z:1 XG:i:0 AM:i:37 NM:i:2 SM:i:37 XM:i:2 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2212:11008:76696 163 chrA02 1060196 60 150M = 1060404 358 TAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACTAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAA @CCFDEFFFHHGGHGIIIFH?CFHIGBFHEHIGHBGHIGGIJIGJJGGHEECFGIGIDFFFHACFADAAE)=EEA))7;;?@ACC https://github.com/ACC?2,;>?AC?DCCDDCDCCDDDD@@BCDBDDDDDDDDDCDDDDACC:ACDABCCDDCDCDDCDBAA X0:i:1 X1:i:0 MD:Z:75A74 RG:Z:1 XG:i:0 AM:i:37 NM:i:1 SM:i:37 XM:i:1 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1107:7944:35767 147 chrA02 1060196 60 100M = 1060092 -204 TAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTADDEEDEDDCCCDDDDDDDDDFFECEFGHHGCGIGHF@JIHD?FFDHFGDHGGEGGIIIIHGGIJIHGEIJIIHFIJIIIJIHJIJIIHHHHHFFFDD@@B https://github.com/B X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2108:16516:46301 147 chrA02 1060196 60 100M = 1060092 -204 TAGGAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTA DDEEDEDDDDDDDDDDDDDDFFFFHHGHHGGJJJJJJJJJJJJJJJJJIJJJIJJJJIJJHHGJJJJJIJIJIHJJIJJJIHJJJJJHHHHHFFFFD@@B https://github.com/B X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2213:17729:66355 163 chrA02 1060199 60 150M = 1060259 210 GAATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGG @CCFFFFFHHHHHJIGIIIGIIJIJJJJIIJIJJJIJJIIJJJJIJIJIIIIHIJJGJHGIIJIJIIJFHHHHHEHDFFFEEDDCCDDDDDDDDDDDDDDEBCDCCDDDDDDDDDDDDDDCDDDDDDDDCDDDDDDDDDDDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2109:9764:31021 99 chrA02 1060200 60 101M = 1060374 274 AATAACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATAT CCCFFFFFHHHHHJHIIIJJJJJJJJJJJJJJJIJJJIJJJJJJJJIJIJJJIJJJJJJJJJJJJJJJJJJHHHHHFFFFEDDEDDCDDDDDDDDDDDDEE X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2113:16946:26277 147 chrA02 1060203 60 150M = 1060128 -225 AACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAG CADDDDDDDDDDDDDDDDDDDDDDDDDDB@DDDDDDDDDDDDDDDDDDCDDDDDDDDEDEDEEFEECEECFFEDBHHHHJHJJIJIJJIIJJIJJJJIJJIJJJJJIIJJJJIJJIGGJIJIJJJJJJJIHJJIGEJHGHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2103:11098:16547 83 chrA02 1060204 60 101M = 1060105 -200 ACTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTT C?DC@@DDDDBB@A@ECEDFEFDHHHGHHIF=JJJIIJIJIGIEGADJJIGIHCIIIHCEJJIIEEGIHHGCEEHEGFC4EFAEEIIGDFHGHFFFFF@CC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1113:12264:49780 147 chrA02 1060205 60 100M = 1060105 -200 CTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTT CCDDDDDDDDDDDEEEEFFFDCHGGHFGJJIIGJJIJJIHJJIJJJJJJJJIIJJJJJIJJJIHEIJJJIJIHIIJJIHJJJIHJJIHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1116:19564:59075 147 chrA02 1060205 60 100M = 1060105 -200 CTCCAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTT DDDDDCDDDDDDDEEDDFFFDCHHGHHIJJJIJJIJJIJIIJIIJJJJIIGGHJJJJJJJJJIIGJJJIGJIHJJJJIJJJJIHJJIFHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1105:18844:34441 147 chrA02 1060208 60 100M = 1060104 -204 CAATTGTGTCGTTAAGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTAC DDDDDDDDBDDCAEEDEDDFFFHHFIJIIGJIIIIIGJJIHJIJJIJJIIIJJJJJJIGHHGGJJJJIJIJJJJJJIJJIIIHJJHFHHHHHFFFFF@@B https://github.com/B X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1207:6648:97615 99 chrA02 1060222 60 101M = 1060373 251 AGCCACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACT CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHIJJJJHHHHHHFFFFF?CEEEDDDDDDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:1116:2037:40290 147 chrA02 1060225 60 99M = 1060074 -250 CACATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCCCCCA?B?DDCB>BEFFCFEHHBGHIJHEHEAHGIIHFCHHGFBCIIGGHDGGIGEIHHGHFGGGFIIGEJJHHIIIJJIJIHGJIGFHFCHFFFDD=? X0:i:1 X1:i:0 MD:Z:99 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1203:17595:58487 147 chrA02 1060227 60 95M = 1059832 -490 CATGTTCCCCTCTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAAC @:B?B>@BAADB;;DE?3CEEHIIEH@C@:HCFD@HCCHFB@HGGEABB?)D>BCGG HWI-ST1026:212:H0APPADXX:1:1108:21038:88529 99 chrA02 1060238 60 150M = 1060396 307 CTGCTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGA CCCFFFFFHHHHHIJJJJIIJJIJIIBHGIJJJJIJJJJJJJJJJIJJJJJIJIJJJJIIIJIJJFGGIJJHGHFFFFEECEEECEDDDD>CCBCCCDDDDCDCCDDBBDDACDACDCCDDDDDDDCCD>CDCCDDDDDDDDCDCDDBDC X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2101:9434:76113 97 chrA02 1060241 37 112M = 1060241 112 CTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAG @@CDFFDFHHHHHJJJGIHIGIEBHIHFHHIICHIAFHC;FGIJIHEHIJJJJJJJJJIJGH8FFH@DEHEHHFFFFFFFEEEEEDDDDDACDDDDDDDDDDBDDDDBDDDD X0:i:1 X1:i:0 MD:Z:112 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2101:9434:76113 145 chrA02 1060241 37 112M = 1060241 -112 CTATCTGCAGAAGAAGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAG DDDDDDDDCDDDDDDDDDDEDEDDC>CC@DEEDDDDBHHHEHEHJHGCJIHFJIJJJJJJJJJJJJJJJIGDIGIJGIHIIFJJJIJJJJJIGJIHGAJHHGGHFFFFD@C@ X0:i:1 X1:i:0 MD:Z:112 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2215:17517:100167 99 chrA02 1060255 60 101M = 1060307 152 AGACAAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAA CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJHHIJJJJJJJJJJJJJJGIJJJIJJJJJJJJJJJJJJJHHHHHHFFFFEEEEEEEDDDDDDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2213:17729:66355 83 chrA02 1060259 60 150M = 1060199 -210 AAAATCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTT DEDDCEDDDCDCCCCDDDDDDBDDEDEDDDDEDCCDEEDDDDDDDDBB=DDCDDCDDDDCCABEEDEEEFFFFDBFHHHEHJJJJJJJJIJJJJJJJJJIHIJJJJJJJIHIJIHIJJIJJJJJIJJIJJJJJJIJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2111:18347:14974 83 chrA02 1060263 60 101M = 1060051 -313 TCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACAT AEDEEDCCDDDDDDDDDDDEEEFEEFFFFFFFHHHHHHJJJJJJIIJJJJJIGJIIIHIIJJJJJJJIJIIJJIHEJJJJJJJJJJJJHHHHHFFDDDCBB X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2208:8732:58355 83 chrA02 1060263 60 101M = 1060021 -343 TCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACAT DEEEDDDDDDDDDDDDDDDEEEFEEFFFFFFFHHHHHHJJJIIJJJIJJJJJJJJJJJJIJJJJJJJJJJJJJJIHJJJJJJJJJJJJHFC1HFFDFDBBB X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2214:12466:18853 83 chrA02 1060263 60 101M = 1060051 -313 TCAGATACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACAT CDEDDCCDCCDDCDDBDDDCCEFECBFFEEFFHHHHHHJIIJJIGJJJJJJHEIIJJIJIJJJJJJJIJIHJJIHFJJJJJJJJIIJJHHHHHFFFDDCB@ X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1207:12415:36278 147 chrA02 1060269 60 150M = 1060172 -247 ACAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAA @CDDDDDDDDDDDDEDEDDCDDDCDEEEDDDDDDDDDDDDDDDDDDDC@DCADDCDDDDCDEEDDEEC@5FFFHGHFHJJGJIIIJJIGBDDIJJIJJIHIHIHIGIJJJJIHHIIIIJJJIJJJJJIHHJJJJJJJHHHHHFFFFFB@@ X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1115:9585:55270 99 chrA02 1060270 60 150M = 1060367 247 CAAGAGCACAGCCACTACACTAACTAAATATGGTTTACGCCTGAACCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAAT @@CFFFFFHHGGHIJI?FFHIJJJJIGEIEIJIGIIHIIIIJFCH@FHIJJJJGGIIIJIIIJJJEHHEHHHDFFFDDCA;CB?ACCD@BADDDD9 HWI-ST1026:212:H0APPADXX:1:1201:17783:76776 147 chrA02 1060276 60 150M = 1060165 -261 CACAGCCACTACACTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATAT ABBBBBCECC@CCCECCCEEECCCBCCBBBBBCCCCCCCCCCC>>BBCCCCCCCCC>DA@>;5BCBBDEEEHHHHHEIIIHF=FGHFGDB@GDGGDBCIIIIIIIGHIIHEIIEIHHGHFBGEGIHGF@IGC+>IHEDFFFDDDDDD@@@ X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:2101:7528:97971 177 chrA02 1060278 37 123M = 1060379 129 CAGCCACTACACTAACTAAATATTGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACT B?@@>CADCACEEDA@ CADCACEEDA@2(C@DDDBC@5A>ACECAC;(@FFEC@EHHHCCCIHE@;GB/JIJJJJIJIIJIGIHEHIGJJJIJIHHHFIGIHJJJJJIHHJJJJJGHHGHFFFFF@CB X0:i:1 X1:i:0 MD:Z:23G99 RG:Z:1 XG:i:0 AM:i:37 NM:i:1 SM:i:37 XM:i:1 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2107:7550:65512 147 chrA02 1060278 60 148M = 1060082 -344 CAGCCACTACACTAACTAAATATGGTTTCCGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACATAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATAT @BBBBDABA:@B https://github.com/B@>BBBED@@A5)&BABBBAB@BBBABBBBBBBAA BABBBAB@BBBABBBBBBBAAABEB@B@=BC@BBBD@EAA??7;1>E@IFFIFIIGGIIGBCDBF@DACDIIGIGCFEIIIIIIIIHHECC:BIHFFG<@CCE3CFDFFFDDB=D? X0:i:1 X1:i:0 MD:Z:28A68C50 RG:Z:1 XG:i:0 AM:i:37 NM:i:2 SM:i:37 XM:i:2 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2212:14817:74520 99 chrA02 1060289 60 150M = 1060446 307 CTAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACAT @@CFFFFFHHHHHJFHHJJIJJJJJIJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJIJIJJJJJJJHFFFDDEEEDCDDDDDDDDDDDDDDDDDDDDDDCDDDDDDDDDDDDDDEDDEEDDDDDDDDDDDDDEEEEEEEDDDDDDDDD X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2212:6899:2989 147 chrA02 1060290 60 98M = 1060145 -243 TAACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGA EAABDEEBAA??A????@AADDDDDDDDDEDDIIIICCADCCAEAEB=6ADDDBDDD@DDB??E9@ E9@FFFFCAF@FA:CAA+<,EE?DDD==D?BD? X0:i:1 X1:i:0 MD:Z:98 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2205:13850:98755 147 chrA02 1060292 60 100M = 1060158 -234 ACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGAT DDDDDCACBDDBDDDBDCEEEFDDFFHHHHGHJIJIIGGIIIJGHHCFJIIJJJIGIJJJHIJJIHFGGJJJJJJIHGGHGHGJJJJHHHHHFFFFF@@B https://github.com/B X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2114:6186:83181 147 chrA02 1060292 60 100M = 1060158 -234 ACTAAATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATDDEEEDDDDDDDDDDDEDEEFFFFFFHHEHHHJJJJJJJJIIJJIHFJJJJJJJJJJIJJJJJJJJIGHJJJJJJJJJIIHIIJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1214:2285:25957 163 chrA02 1060297 60 150M = 1060443 296 ATATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTAC CCCFFFDFHHHHHIJJIJJJJJJJIIJJIJJIIEIJJJJJJJIJIIJJIJJJIJJJIJJJJHHHHFFDFDCCEEEDDDDDDDDDDDDDDDDDCDDDD@CCDACCDDDDEDDEECCDDDDDDBDDDDEEDE@DEDDDDDDDDDDDDDCCDD X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1107:1629:12979 163 chrA02 1060299 60 100M = 1060414 216 ATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAAB@@FDFFFHHHHHJJJJJJJJJJIJJJJJJJJJJIJJJJJJJJJJJJJJJIIJJJJJJJJHHHHFFFFBCEEEEDBDDDDDDDDDDDDDDDDDDDCDDDD X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2202:6841:49791 163 chrA02 1060299 60 100M = 1060414 216 ATGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAABCCFDFFFHHHHHJJJJJJJJJJJIJJJIJJJJJFIJJJJJJJJJJJJJJHIJJIIJJJJHHHHFFFF;@EEEEDDDDDDDDDDDDDDDDDCDDDCCDDD X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2214:2410:6771 163 chrA02 1060300 60 100M = 1060465 266 TGGTTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACBCCDFFFFHHHHHJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJJJJJJIJJJJJJJJJJHHHHFFF@CEEEEDDDDDDDDDDDDDDDDDDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1102:4326:6062 163 chrA02 1060303 60 100M = 1060450 248 TTTACGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJGHHHHEFFFFFDDDDDDDDDDDDDDDDDDCCDADDDDDDDD X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2215:17517:100167 147 chrA02 1060307 60 100M = 1060255 -152 CGCCTGAATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATT DDDDDDDDDDDDDCEEEEEFFFFFFEEHHHHCJJIJJJJJJJJJJJJJJJIGGFJJJJJJIIHGHHIIJJJJJJJJJJJJJJJJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2108:21242:47830 99 chrA02 1060313 60 101M = 1060555 342 AATCCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTA @@CDFDDFHHHHHJJGHIJIIJHJJHHIJIIJJIIJHGGHFHIIJIIGGGGIJJ;@=DEHIHHHEDFFFEEEDEDDDD;ACACDCDDDDDACDDDEDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2106:2894:61273 99 chrA02 1060316 60 101M = 1060423 207 CCTAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACC CCCFFFFFGHHHHJJJIIJJJJJGIIJJJJIJJIJJJJJJJJIJJJJJIJJBCGGHIJJHHHHFFFFFFDEECDDDDDCDDDDDDDDDCEDDEEDDDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1115:16779:37508 83 chrA02 1060318 60 101M = 1060172 -247 TAACTCTTGGAAGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAA DECDDDDDDDDDEEDFEEEE?FFFHHHHHJJJJJJJJJIIIHHJIHJJIHFHFHEHFIJJIJJJJJJJJJJJJJJJJJJIIJJJJJIJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1207:17668:59616 163 chrA02 1060329 60 149M = 1060398 220 AGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAG @@@BDDDA2=AFHHGGEGHHCFDCBGHHAG:?FB@FHCHFEGGIGCGIIG;FHHGIGCHHEE>;B.;@CC;>>@CC:@ADAA>@A https://github.com/A:CCCBC@CC;>@>C@A4>CCCCCCA>4>:>>CCCCCC@@ACCCCCC?BBBB@CBC?<@?BBCCA X0:i:1 X1:i:0 MD:Z:149 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1201:20262:94395 163 chrA02 1060329 60 150M = 1060398 220 AGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGC CCCFFFFFHHHHHJIJIJJJIJJJJJJIJJIJIJGGIF9BBHGGGIIJJJIJJJJJJIHGGHH@C;@DEECCEEDD@CCDEDCCDDCDDDDDDDEEDEEEECDDDDDDCDDACDDCCDDDEDDDDDDCDDDDDDDDDDDDDD28?BDDDC X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1206:6192:16029 99 chrA02 1060329 60 150M = 1060404 220 AGAAACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGC BBCFFFFFHHHGHIJJJJIJJJJJIIJJJJJIIJIJJIBGHIJJJIJJIIJJJJJJJJHHHHHFFBEDEEEEEEE@CDDEEDDDDDDDDDDDDCDEEEEEECDDDDDDDDDDDDDDCDDDEDDDDDDDDDCDDDDDDDDDBD+2<@CDDC X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2209:2254:80117 99 chrA02 1060332 60 101M = 1060552 320 AACTTTACCCAAAAAGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAA CCCFFFFFHGHHHJJJJJIJHIJJIIIEIGIJJEG* ?GHEGGJJJIJGGIIJJJHIJGHFFEHFFFFFFEEEEDEDEEDCDDDCACBDDDDDEFF@DDDCA X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1112:21089:55235 99 chrA02 1060346 60 101M = 1060508 262 AGGAAAGAAAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTAC B@CFFFFFHHHHHJJJJJJJJCHHIJJJJJJJJJIJIIJJIIJJGIIJIIIJJGCGGHIJJJHHHHHHHCFFFFCEEEEDFCDDDDDDDDDDDDDDDDDCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:1209:10213:95408 99 chrA02 1060354 60 101M = 1060521 267 AAAAACACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACAT CCCFFFFFHHHHHGHIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJJJJJJJJJJJJJJJJJHHHHHHHHFFFFFEEEEEEEDDDDDEDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1109:5848:65355 99 chrA02 1060360 60 101M = 1060448 188 ACATGGGTACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAA CCCFFFFBFHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHHFFFFFFEEEEEEEDDDDDDDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1115:9585:55270 147 chrA02 1060367 60 150M = 1060270 -247 TACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAA CAAABCCDCEDCCBC>CCCDCCCCCCCCEDC>CCCCCCCCA>CACCBCA@A>BDDDCCECEC@EED @@@FFDBEEHC=.DCG@ADCIHGECEGHGHBHGFEIIIIIIIIIIGHIIIGIIIIIGIIIGEIIGIGGGEBFCFHFDDDDDCC@ X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2110:4171:41120 147 chrA02 1060368 60 150M = 1060187 -331 ACACACACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAAC ??BDCDEDEEDDDDDDDDEDDCDDDDDEDC@DDDDDDDDBDDDDCBDCCEDDFDDDDCAEECEDDEEFFFFFEHHHHEEHGCEGJIIJJIHFDJJJJJJJJJJJJJIIJIGJIIIIJIJHJJIJIIJJJJJJJJJIIHHHFHDDFFFB?@ X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1207:6648:97615 147 chrA02 1060373 60 100M = 1060222 -251 CACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTEEEEEEFFFFFHHHHHHJIJJJJJIIJJJJJJJJJJJJJJJJIJJJJJIHGIHGJIHJIIHIHJIJJIHJIIHJIIJIHJJJJJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1105:6235:32755 147 chrA02 1060373 60 150M = 1060176 -347 CACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGAT DDDCDCC?CDC@CA:ADDDDCDDCDCCC>>>CCDDDCC@ADCDDDDDDCEDCDDC>5@3>CA@ @CAEDEFDA;BAA=E?CEGGGHD;@IHCGFCIHBIIIIHEEIGGJIGJIJIGIIHIGGFIJIJJJIFIIIGIHEFCGFDDDDDD<@? X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2109:9764:31021 147 chrA02 1060374 60 100M = 1060200 -274 ACAATGCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTCDEEEEFFFFFFHHHHHHIIIJJIIJJJJJJIJJJJJJJJJJJJJJIJIIIHIIIGIIIGHGJJIIIIJJIHJJIIJHJJJJJIJJJHHHHHFFFFF@CC X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:2101:7528:97971 113 chrA02 1060379 37 151M = 1060278 -129 GCAACAAGAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAA CDDCDDDEDDDDDDDDEDDCDDDDDDDDDDDDDDDDDDEEEFFEDDDDCDCDEEDCCDDDCDCDDFEEEEDDDFFFHGHHHIJJJJJJJJJIIJJJJJJJIJJIHJJJJJJJJJJJJJJJJJJJJIJJJJJIIJJJJIHHHHHFFFFDCCC X0:i:1 X1:i:0 MD:Z:151 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1214:16561:14629 147 chrA02 1060386 60 100M = 1060187 -299 GAAGATGGTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACG EDDEEEEEEFFFFFFFHHHHHHJJJJJJJJJJJJJJIJJJIJIGJJIIHHIIIJJIIHGGJJIFHFJJIJJJJJJJJJJJJJJJJJJHHHHHFFFFF@CB X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:1208:13246:82013 163 chrA02 1060393 60 100M = 1060558 266 GTTAAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATT CBCFFFFFHHHHHJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJIJJJJJJJJJIIIJHEHHFFFFFFEEEEEDDDDDDEE X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1108:21038:88529 147 chrA02 1060396 60 149M = 1060238 -307 AAACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAA CDDDCDDDDDCDDCCCDDDDDCC>EDACC@ACDCDDDCDDCA>CDCCC@

3EDEEDDDDAEEEEEFFFFFHHHGIIHDIIIIHGIHAHGIJHHHGEIGGDHIGIIIGGJIIIHIIGHHHCJJHCIJJJJHIJIJJJHHHHHFDDBFB@ X0:i:1 X1:i:0 MD:Z:149 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1105:20897:68893 99 chrA02 1060398 60 151M = 1060541 293 ACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGG C@@FFFFFGHHHHJJJJJIEIJJJJGJIIB?HHGIGJJII@FHHBFIJJJJJIIGIIJGIJJJJJJIGIJIFI5 =AHHGFHFFEEFEBABB@CFCDDD:ACA:B5:@CDDDDDDCDDDDDBDDDDCC@C@CDDDDDE@CDDDDDCDDCDDA X0:i:1 X1:i:0 MD:Z:151 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1207:17668:59616 83 chrA02 1060398 60 151M = 1060329 -220 ACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGG AC@CC>@3C?:@CC>DC@EDCC>3C@>C@@>DA:CCCCAC@ ;>5>@CC>5>CACCCCA;CCCCEBB?BECCEDA=@AC https://github.com/AC@@;;EGIGAFB?@GIHDGHFHHCCDCDEEGC?GEDC HWI-ST1026:212:H0APPADXX:2:1201:20262:94395 83 chrA02 1060398 60 151M = 1060329 -220 ACTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGG DDDDDCDDDDDDDDCBCCCEEDCDEDDDEDDCCDDDC@DCCDCDDCCBCCDDEDDDDDCDDEADDECCEFFHHHEGDIGACHIJHFJJJJJJJIJJIJJJGIJIHFGHIIJIJJIIIHHJIIGIIGJDEEJIJIJIHGFHFFHFFFFFCCC X0:i:1 X1:i:0 MD:Z:151 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1203:19183:45186 99 chrA02 1060399 60 101M = 1060514 215 CTAGCATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAAT CCCFFFFFHHHHHJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ;CHHHHHHHFFFFFDDDDBDFFFED@CDD X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1213:4390:19969 99 chrA02 1060403 60 142M = 1060488 217 CATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAA ??DD:,,=C222BEB>ECCDFICEDCDEEEIIC<*_0?D;=BADII;@CA https://github.com/CA @CDCACAA@@4 https://github.com/4'3BBA>:>A>>>D::>>>>:>A>(>814:44>AA>AAAADDA43>8:>AA X0:i:1 X1:i:0 MD:Z:142 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1101:11651:60111 163 chrA02 1060404 60 100M = 1060497 194 ATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGG CCCFFFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJJJJJIJIJJIJJJJJJJJJJJJJIIIJJIJJCGHIJIHHHHHHHFFFDDBDEEEEDACDDDFED X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1108:19842:60942 163 chrA02 1060404 60 150M = 1060448 194 ATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGGTATCA CCCFFFFFHHHHHJJIJJJJJJJIJJJJJJJJJJJJJJJJJJJJJIHIIIJJIIJEGHHIIJGIHHGGHIJJIHGHGHHGFFFDD?CDDDED;@CAC @DCC>CDDDDDDDDDDDDDDDDDCCACDDCDDDEEDDDDDDDDDDEDD9@CCD X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1215:13369:6978 163 chrA02 1060404 60 150M = 1060533 280 ATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGGTATCA CCCFFFFFHHHHHJJGIJJJJJIJGJGHJJFGIIEGGIIIIIJJJIJIJJIJGIJJJIJHJIEHIIIBFHIIJECHGFHGFFFCB?CEFEEDCDDEDDEDDACCDDDDDDDDDDDDDDDD>C>CDDDDDDEEDDDCDDDDDDEDDACDDE X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1206:6192:16029 147 chrA02 1060404 60 145M = 1060329 -220 ATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGG @A https://github.com/A>>@>::4@ :++(:>4:4:,((5:>;@;:;@;5-;>;5>?DEBA>ECB;6=HHCHC@7=:5=CGHG@?D??84DDBB?0>B_EEHF HWI-ST1026:212:H0APPADXX:2:2212:11008:76696 83 chrA02 1060404 60 150M = 1060196 -358 ATTTTCTTTAACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGGTATCA ACCBCADDCAA:CEDBC>DADC@CDDDEEEDCADDDDCCCFD@;CADC@@ACDDDDBDDCC@ ?CBFFCDGHHFHE@IIIHIIHIIGIIIIIIIIIIIIGGB9IIGEHGIIHHBIIIIGIIGIHHHH @HDIDCEEGGFDHHFDDFFFF@@@ X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1107:1629:12979 83 chrA02 1060414 60 101M = 1060299 -216 ACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCA DDDEEEFEEEEEEEEFFFFFECHHHHHJJJIHJJJJJJJJJJJIJJJIJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJHHHHHFFFFDCCB X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2202:6841:49791 83 chrA02 1060414 60 101M = 1060299 -216 ACCAATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCA DDDDEDDEECEEAEEFFFDBFFHHHFHGJIGGIIGGGCIHGIEJIJJJIJJIIGEJIJIGIIIIIHJIIHJIIIIJJJJIGJIJIIJJHHHHHDFFFFCCC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1213:6755:36173 163 chrA02 1060418 60 150M = 1060442 175 ATTAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGGTATCATGAGAAATGCAGTA @CCFFFFFHHHHHIJJIJJJJJJJJIJJJJJIJIJJJJJJJJGIIGIIIJHIIFGHIIJIIEGIJIIJJJHCHFFFFFCDEEEDCCEDDDDDCDDDDDDDDBDDDDDDACDCDDDDEEDDDDDDDDDDEDD>@CDDEDDDDDDDDDDDDD X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:1116:10277:36351 99 chrA02 1060420 60 101M = 1060573 253 TAATATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAG CCCFFFFFHHHHHHHIIIFHIIJJJIJJJJJJJJJJJJJHHHIJJJIIIJJDFHJJIJJJJIHJHHIIHCHCEHCF7@DDE@DDEEEDDDDDDDDBBBDDA X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:2:2106:2894:61273 147 chrA02 1060423 60 100M = 1060316 -207 TATTCTACAATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATDDDDDDCDEEDC@EEAEFDFFFDFGHEEEGHHIJIJJIJJJJJJJIJIGIIGJJJJIJJJIJJJIJIIJJIJIIIJIJJJJJJIIJIHHHHHEDFFF @C@ X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2213:1551:33430 99 chrA02 1060432 60 150M = 1060506 224 ATCACATGCTCTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGGTATCATGAGAAATGCAGTAACAACCACAGTCAT CCCFDFEDHHHGHIIIIIIDGHGIAGHIIIIIIIH;FG>0?FFHIHIIIIGIIIIIHHHIIIBHCGIHHEHHGHFFEFFFCEECCCBCBCCC>A>CCCCCC@CECCCCCCCCCCECB?ACCED:AACCCCCCCCCCCCCCBBBCBBCCCE X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1213:6755:36173 83 chrA02 1060442 60 151M = 1060418 -175 CTTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGGTATCATGAGAAATGCAGTAACAACCACAGTCATCATCACCATCT CDDBCDC>CADEDDCDDDDDDDDDDDDDDDDDDDDDDDDDDDBCEDDDDDDDEECEEEFFFFEDFGHEE?IJJJIJIGIJIIIHGIJJJJJIHFJIHHGHJJIGIJIJJJJJJJJJJJJIJJJJIIHGGHIHIJJJIJHHHHHFDFFFBC@ X0:i:1 X1:i:0 MD:Z:151 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1214:2285:25957 83 chrA02 1060443 60 150M = 1060297 -296 TTACTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGGTATCATGAGAAATGCAGTAACAACCACAGTCATCATCACCATCT CDCCDEEEEDEEDDDDDDDDDCDDDDDCDDCCDDDDDDDDDDDEDDDCDDDEEEEEEFFFFFFFHHHHHIGIIGJJIJJJJJJJJJJJJJJJIIIIIIIJJJIJJJIJJIJJJJIJJJIJJJIJIIIHGJIJJJJJJHHGHGFDFFFCCC X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2212:14817:74520 147 chrA02 1060446 60 150M = 1060289 -307 CTTACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAAATGTGACAATAAATACAAACTAAATGGGTATCATGAGAAATGCAGTAACAACCACAGTCATCATCACCATCTTTG CEEEEDDEDDDDDDDDDDDDDDDDCDDDDDDDDDDDDDDDEDDDDDDCCDDDEEEECEFCFFFFFHHHHEEAB=)IIGHGGIJGIJIIIFIJJIJJJJIJIJJIJJIIJJIJJJJIJIIIGIIGG@IHHIJIJJJJJHHFCGFFDDFCB@ X0:i:1 X1:i:0 MD:Z:74G75 RG:Z:1 XG:i:0 AM:i:37 NM:i:1 SM:i:37 XM:i:1 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:1109:5848:65355 147 chrA02 1060448 60 100M = 1060360 -188 TACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGEDDDDEDDDDEEEEEFFFFFHHHHJJIJIJIHJJIFJJJJJJJJIJJJJJJJJJJJJJJJJJJIJJJJIJJJJJJJJJJJJJJJJJIHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:100 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:1:1108:19842:60942 83 chrA02 1060448 60 150M = 1060404 -194 TACACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGGTATCATGAGAAATGCAGTAACAACCACAGTCATCATCACCATCTTTGTT EDEEDEEDDDDDDDDDDDDDDDDDDDDDDDDDDDDBDDEDDDDDDDDCADDDEEEEEFEFFFFDHHHHHJJJJJJJJIHJJJJJJIHEJJJIJJJJJIJJJJJJJJJJJJJJJJJIGJJJHJJJJJIIJJJJJJJJJHHHHHFFFFFCCC X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U DD65WKN1:82:H0KAMADXX:1:2206:13121:34817 99 chrA02 1060450 60 101M = 1060521 171 CACATAGCAAACAAAAGAGGGTTTTCAGCTCAAACGCAGTATTAGGTAATGTGGAACTATAACCAAACCAGATGTGACAATAAATACAAACTAAATGGGTA CCCFFFFFHHHHHJJJIIIJJCHIJJJJJJJJJJJJJJJFHJJJJJDGIJJIJJJIJJJJJJJJJJHHHHFFFFFFEEEEEEDDEEDDDDDDDDDDEDDAC X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM

[genecao]

Hi Ryan,

attached is the bam file slice and the error report is: Error removing element:chrA02,1059879,1060298,- chrA02,1060400,1060399,- 1 Aborted (core dumped)

On Tue, Aug 26, 2014 at 4:28 PM, Ryan Layer notifications@github.com wrote:

I am having a little trouble parsing this when pasted into an email. Can you make a new bam file that contains these alignments (command below) and email them to me at rl6sf@virginia.edu?

samtools view -b sample.bam chrA02:1058000-1061000 > slice.bam

On Tue, Aug 26, 2014 at 2:54 PM, genecao notifications@github.com wrote:

here is the details:

Error removing element:chrA02,1059879,1060298,- chrA02,1060400,1060399,- 1 Aborted (core dumped)

bam slice:

HWI-ST1026:212:H0APPADXX:1:2206:1146:42729 163 chrA02 1059833 60 150M = 1060083 400

GCTTTGACGCCCTCTCCTGCACATTCTCTTGTGTGGTCTCCACTGGGTGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGT

@@@DDD https://github.com/DDD?DFHHHH@GGGIIIIGHGIGGIGIIHIIIIGGHIIIGIII

=BFHFIIIIIIIIIIIHFFFEEEEECCCBCDCCDCCCBBBBBBCBBBBBCCCCCBBCBBCCCCCB?CCBCCC@CA9BBCCCCBBBBB@4:?BBBBCBCCB?

X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1110:9185:96275 83 chrA02 1059849 60 139M = 1059761 -227

CTGCACATTCTCTTGTGTGGTCTCCACTGGGTGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAG

CCA:(:AA9BCB@@??1C8?@:??88CCB>44@C>A>>55<4C:@4 https://github.com/4 :A909@>?;9(9DFFFFHAD=EA@@AC https://github.com/AC@CGFB HWI-ST1026:212:H0APPADXX:2:2215:6410:81755 145 chrA02 1059853 37 148M = 1059857 -144

TCTTTCTCTTGTGTGGTCTCCACTGGGTGCTTCCCCCATGGACAAAGCTCTTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCTCAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCA

ACCC?BCBBBBBA?@BCBCCCCBBBBCCBB3>(33:+:DCCCBB>9@BA88BB ?CCCCCECEB?AA=CAEC@7 ;:IGIGIHF9B)FB?670)3:

*BB9 HWI-ST1026:212:H0APPADXX:2:2215:6410:81755 97 chrA02 1059857 37 146M = 1059853 144

TCTCTTGTGTGGTCTCCACTGGGTGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATG

@@DDDDDHFCDHIDGBFHG4AAF+=B>?CCCCCBBCB?ACCCCBCCCBCCCCC@BBB>9ACBBBBB<((44:<?092>?ACB<?C?CCCCCCACABBBACC>C

X0:i:1 X1:i:0 MD:Z:146 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:1205:4838:65174 147 chrA02 1059869 60 150M = 1059829 -190

TCTCCACTGGGTGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTG

CDDDCCDDBDDCDB@@BDBDDBCDDDCCADDDDDDEEDEDCC>BB@ BB@89<@BDCDDCADDFDDCC@CCCECCEDED @?DFBHHHEJIIIJIJIHJIIJJJJIFIJJJJJJJIIIIJJJJJIIIJJJJJJIJJJJIGHHHHHFFFFFCC@ X0:i:1 X1:i:0 MD:Z:150 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2114:15536:39752 147 chrA02 1059871 60 150M = 1059753 -268

TCCACTGGGTGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTC

CDCADDDDDDDDDDDDDDDDDDDDDDDDDDDDDEDDEDDDB>DDDDA@@ HWI-ST1026:212:H0APPADXX:2:2203:12594:32130 99 chrA02 1059880 60 151M = 1059953 223

TGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTCGTATGAGTAGAAAGGCATCATGTGGACAAAAATATCTGTCGTCTCCATAG

@CCFFFFFHHHHHJJJJJJJJJJIIIIJJJJJJIJJJJIJJJJIHIJJIIGGGHGFFFFCEEEDDDDDDDDDDDDBDDDDDDDDDDDDDDCC?BDDDDDDD?@BDDDDCDDDDDDDDDDDDDDEDDDDDDDBDDDEEEEDCBBDDDDDDDA

X0:i:1 X1:i:0 MD:Z:151 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0

XT:A:U DD65WKN1:82:H0KAMADXX:1:2106:4807:69648 83 chrA02 1059880 60 101M

1059745 -236

TGCTTCCCCCATGGACAAAGCTCGTACTTAAATCCCCGCATCCGAGCAAAATCGAACTGACAGCAAACTGCAGGCTCAGGCCCACAAGTGTGTGGGATGTC

DDDDDDDDDDEDDDDDDDDDDDDDDDDEDDDDDDDFFHHJJIJJJIJJJJJJJJJIJIJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJHHHHHFFFFFCCC

X0:i:1 X1:i:0 MD:Z:101 RG:Z:1 XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 XT:A:U HWI-ST1026:212:H0APPADXX:2:2106:13655:65622 147 chrA02 1059883 60 150M = 1059822 -211

[genecao]

I played with it a bit more and found that if you set the read_length shorter or equal to the min_non_overlap the error goes away.

[ryanlayer]

Yes! Read_length and min_non_overlap should, in the vast majority of cases, be the same and both be the length of your reads.

On Wed, Aug 27, 2014 at 9:21 AM, genecao notifications@github.com wrote:

I played with it a bit more and found that if you set the read_length shorter or equal to the min_non_overlap the error goes away.

— Reply to this email directly or view it on GitHub https://github.com/arq5x/lumpy-sv/issues/33#issuecomment-53570923.

Ryan Layer

[jjfarrell]

For my example above, the read_length and min_non_overlap were both set to 100.

[ryanlayer]

This was caused by an alignment with a CIGAR string of "100I", which makes no sense. I have since added a check to ensure a CIGAR string has at least one match.