Open ghost opened 7 years ago
ocxtal
commented
7 years ago Hi @aderzelle,
Thank you for testing my software and the potential bug report.
Would you tell me the commit hash (or version number if you have installed it with bioconda)? It might be a bug but several known ones (which caused the similar memory error) are fixed in the current master. I would also appreciate if you could upload the actual PacBio dataset somewhere.
Thanks in advance,
Hajime Suzuki
ghost
commented
7 years ago I installed minialign yesterday from github, so I guess it's the current master version (I am not sure this answers your question). I can send the Pacbio file, do you prefer fasta or fastq? And where do you want me to send them?
ocxtal
commented
7 years ago It seems your binary is the newest version. Thanks for the information.
The file may be too large to be attached to a mail, I prefer you to upload it to some uploader, like google drive, and send me (suzuki.hajime.s@gmail.com) a link to it. I think fastq format is better since I can convert it to the other but I need the identical one to reproduce the problem.
Thanks,
Hajime Suzuki
ghost
commented
7 years ago I am sending you a wetransfer link.
Thanks
ocxtal
commented
7 years ago I've been waiting for the mail received but it seems to have a trouble. Could you send another mail (without link) or paste the link to the uploader here (if possible).
Thanks,
ocxtal
commented
7 years ago I've successfully received the file. And I have missed the important question: what is the reference sequence did you use?
Thanks,
ocxtal
commented
7 years ago Could you tell me the command line parameters that you got the problem (for example $ minialign -t8 -xpacbio hg38.fa pacbiodataset.fq.gz > out.sam) and the output of $ minialign -v (which shows the version number like 0.5.2-5-g78c9e7b)? And it will also be helpful if you could figure out the compiler version (gcc -v), operating system (cat /etc/*release if you use linux), and processor model (cat /proc/cpuinfo on linux).
ghost
commented
7 years ago this was the command line
minialign -l vaga_index.mai SubPacbio.fq > out.sam
The version is 0.5.2-10-g00b8740
The gcc version
gcc version 6.3.1 20170306 (GCC)
I am using Manjaro Linux and the processor is the Intel(R) Xeon(R) CPU E3-1505M v5 @ 2.80GHz
I am sending you the reference.
ocxtal
commented
7 years ago I have updated the master to d46ffb7 and please try it as follows:
git pull origin master
make clean && make
make install PREFIX=...In my environment with Ubuntu 17.04 and gcc-6.3.0, the 0.5.2-10-g00b8740 binary segfaulted (by somehow a different reason) but the current master 0.5.2-13-d46ffb7 successfully produced a 31GB sam file. Actually I wrote the patch for another SEGV but it seems work well for your data on my environment.
But it's just a brief survey so there still be a possibility of another bug. Please notify me if you still encounter the SEGV with the updated one.
Thanks,
Hajime Suzuki
ghost
commented
7 years ago It works! thank you. However main converting to bam it gives the following error
[E::sam_parse1] CIGAR and query sequence are of different length
The resulting bam seems mostly usable, as only some lines seem affected.
thanks for your help.
ocxtal
commented
7 years ago Thank you for your report. I tested several parameters including -xont and -xpacbio on your data on several machines but I couldn't reproduce the error. Could you tell me the command line parameters and the line number? (samtools outputs line number in the input sam file where an error detected; in fact the actual sequence name or sequence is more helpful if you could figure out it)
ghost
commented
7 years ago minialign -l vaga_index.mai SubPacbio.fq > out_minialign.sam
samtools view -@ 6 -bS out_minialign.sam|samtools sort -@ 6 -o out_minialign.sorted.bam -Samtools says
[E::sam_parse1] CIGAR and query sequence are of different length
[W::sam_read1] parse error at line 571125
[main_samview] truncated file.The start of the offending line is as follow
m161225_173109_42202_c101087462550000001823263803141737_s1_p0/1950/0_14634 0 scaffold_151 309436 60
ocxtal
commented
7 years ago Hmm...
I tested the following command and got no error. The problematic sequence and two neighbors were extracted and aligned by minialign-0.5.2-13-gd46ffb7 onto the raw fasta then sorted. (note that minialign.head is aliased to the current head of master in my env)
12:51:23 [ryzen] /data/seqs/debug % zcat /acv/seqs/debug/SubPacbio.fq.gz | grep -11 "m161225_173109_42202_c101087462550000001823263803141737_s1_p0/1950/0_14634" | tail -20 > ext.fq
12:56:46 [ryzen] /data/seqs/debug % minialign.head -t16 /acv/seqs/debug/vaga_sub.fa ext.fq > ext.minialign.head.sam
[M::mm_idx_gen::0.883*4.51] collected minimizers
[M::mm_idx_gen::1.350*5.08] sorted minimizers
[M::main::1.350*5.07] loaded/built index for 1376 target sequence(s)
[M::main] Version: minialign-0.5.2-13-gd46ffb7
[M::main] CMD: minialign.head -t16 /acv/seqs/debug/vaga_sub.fa ext.fq
[M::main] Real time: 1.914 sec; CPU: 7.483 sec
13:01:18 [ryzen] /data/seqs/debug % samtools view -@ 6 -bS ext.minialign.head.sam | samtools sort -@ 6 -o ext.minialign.head.sorted.bam -
13:01:26 [ryzen] /data/seqs/debug % Still there is a possibility of a bug so I'll inform of you when something is found.
Thanks,
ghost
commented
7 years ago Hello,
I have launcher the analysis on a Ubuntu machine and I have no error. It seems to be linked to my Manjaro distribution. But the important point is that I succeeded to use minialign. Thanks a lot for your assistance.
ocxtal
commented
7 years ago Thank you for your report and using minialign.
Actually unknown SEGVs, especially SIMD- and compiler-backend- (optimization) related ones, are often found when I upgrade some linux components so it might be. I'll try some Arch / Manjaro images later for another testing environments.
Thanks,
smallwhitelama
commented
6 years ago When Version :0.6.0 , I also have the same problem.
# minialign -t 32 index.mai reads.fastq -O blast6 > minialign.out.sam
[M::main_sse41] Version: 0.6.0-devel, Build: SSE4.1 [M::main_align::12.370*1.15] loaded/built index for 22351 target sequence(s). Error in `minialign': malloc(): memory corruption: 0x00007fd60c00a8f0 ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fd66ad767e5] /lib/x86_64-linux-gnu/libc.so.6(+0x8213e)[0x7fd66ad8113e] /lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x54)[0x7fd66ad83184] minialign[0x41f9e0] minialign[0x4a6727] minialign[0x42856f] minialign[0x42924e]
but when I use the version is 0.5.3 , minialign can work.
[M::main::11.883*1.09] loaded/built index for 22351 target sequence(s) [M::main] Version: minialign-0.5.3-unknown [M::main] CMD: minialign -t 32 -l index.mai reads.fastq -O blast6 [M::main] Real time: 407.492 sec; CPU: 9314.120 sec
ocxtal
commented
6 years ago It seems the current HEAD complete the task correctly on my environment. I'm running valgrind on the same task but it takes overnight to get the result. Can you tell me the commit hash of minialign you used (just to make sure the version is the same).
18-04-12::10:50:23 [ryzen] /data/seqs/debug % minialign -t16 -d vaga_sub.fa.mai /acv/seqs/debug/vaga_sub.fa
[M::main] Version: 0.6.0-8-ge0fcec1, Build: AVX2
[M::main_index::2.841*3.00] built index for 1376 target sequence(s).
[M::main] Command: minialign -t16 -d vaga_sub.fa.mai /acv/seqs/debug/vaga_sub.fa
[M::main] Real time: 4.475 sec; CPU: 31.785 sec
18-04-12::10:50:30 [ryzen] /data/seqs/debug % minialign -v
[M::main] Version: 0.6.0-8-ge0fcec1, Build: AVX2
18-04-12::11:28:43 [ryzen] /data/seqs/debug % minialign -t16 vaga_sub.fa.mai /acv/seqs/debug/SubPacbio.fq.gz > /dev/null
[M::main] Version: 0.6.0-8-ge0fcec1, Build: AVX2
[M::main_align::0.673*9.68] loaded/built index for 1376 target sequence(s).
[M::main_align::690.995*15.95] finished mapping `/acv/seqs/debug/SubPacbio.fq.gz' onto `vaga_sub.fa.mai'.
[M::main] Command: minialign -t16 vaga_sub.fa.mai /acv/seqs/debug/SubPacbio.fq.gz
[M::main] Real time: 691.038 sec; CPU: 11019.556 sec
18-04-12::11:40:35 [ryzen] /data/seqs/debug % ~/docs/src/minialign/minialign -t16 vaga_sub.fa.mai /acv/seqs/debug/SubPacbio.fq.gz > /dev/null
[M::main] Version: 0.6.0-10-g336091e, Build: AVX2
[M::main_align::0.661*9.82] loaded/built index for 1376 target sequence(s).
[M::main_align::691.775*15.98] finished mapping `/acv/seqs/debug/SubPacbio.fq.gz' onto `vaga_sub.fa.mai'.
[M::main] Command: /home/suzukihajime/docs/src/minialign/minialign -t16 vaga_sub.fa.mai /acv/seqs/debug/SubPacbio.fq.gz
[M::main] Real time: 691.817 sec; CPU: 11051.584 sec
18-04-12::12:33:55 [ryzen] /data/seqs/debug % ~/docs/src/minialign/minialign -t16 -Oblast6 vaga_sub.fa.mai /acv/seqs/debug/SubPacbio.fq.gz > SubPacbio.minialign.txt
[M::main] Version: 0.6.0-10-g336091e, Build: AVX2
[M::main_align::0.662*9.82] loaded/built index for 1376 target sequence(s).
[M::main_align::687.701*15.97] finished mapping `/acv/seqs/debug/SubPacbio.fq.gz' onto `vaga_sub.fa.mai'.
[M::main] Command: /home/suzukihajime/docs/src/minialign/minialign -t16 -Oblast6 vaga_sub.fa.mai /acv/seqs/debug/SubPacbio.fq.gz
[M::main] Real time: 687.748 sec; CPU: 10984.663 sec
18-04-12::12:45:38 [ryzen] /data/seqs/debug Thanks,
npavlovikj
commented
6 years ago Hi,
I am not sure if this is related or not, but for some nanopore sequences with minialign 0.5.3-325-g336091e I am getting: "** glibc detected minialign: free(): invalid next size (fast): 0x00000000023f5710 *" with similar Memory map as above. On the other hand, the same sequences work well with minialign 0.5.2. The commands I am using are: _minialign -d index.mai ecoli_K12MG1655.fasta minialign -x ont.r9.1d -O sam -T MD,AS,NM index.mai 1.fasta > 1.sam
Please let me know if you need any additional information.
Thank you, Natasha
EDIT: From the sequences that threw the "glibc" error, if I remove only the first or the second nucleotide, the alignment finishes successfully. I haven't observed any pattern with these nucleotides yet, but is it possible that some border case is maybe missing?
ocxtal
commented
6 years ago Sorry for being late. May I ask you to paste the sequence and the (whole) reference that raised the error? (If the reference sequence is not modified from the original MG1655 assembly I already have the same one.)
I think it is likely a boundary violation error in the SAM formatter, but I can not be sure until I see actual data. The notion that removing the first base avoids the error is really helpful.
Thanks,
npavlovikj
commented
6 years ago Hi @ocxtal,
Thanks for getting back to me.
Please find below 2 E. coli sequences. I used the E. coli K12 MG1655 reference from NCBI, so I believe that is the one you have as well. $ cat 2158.fasta
U00096.3_1467868_aligned_1 ACTGGCCCCCTGAATCTCCAGACCCCCAATATCACTTAAATAAGTGATATTTACTAAGTTTATAGACTAGCAATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACAGCGTACTGCACAGGAAAAGAGCAATGTTCAGCAGAGCTGAACCCTGGGAGACTGTCCCTCGTTGCCCGGCGACAGGTGGTCAGCCAGCTGTTATTTCTCTGGCGTGAAGCCTAGGAAAAGCATTTTACTCTGTGCCGCCGGGAACAGGCAGATGAGTTGGCGGTCCCTTTCGCTGCCGCCATGAAGCCTTAAACAACTCCCGTCTGCTCGGCAAGAAAACGTATGGAAAATGAACTCCTCAAAGAAGCCGTTGAATATGGACGGGCAAAAAAGTGGATAGCGCCCGCGCCCTTATTGCCCGGGGATGGGAGTAAGCTTAGTCAGCGTTTTCTCCGGGTGTCGGGCGCAGTTGCACGTCATTCTCCACGAACCGATGTGGAGGCTGGTCCGGAGCAGTCGTCACTGATGATACGGTGTGCTTCTCCGTCCATATGATATCGGAGAGCTCAGTATGGTTATCGTCAAACCTGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCACGCATTTACCGGATCACTGGCAAATGCGCTGTTGTTGAGCGAAAACCTGTACCGCAATGAAACGGGCAGTGGCAGGCAGAGTGGCCGTGAAAGAAAGCAATCAGCGATGGTGCTCTGACGGGTTCGAGTTCTGCTGATAACGGAGACGAGCTTGAAAGTGCGTTCCGCGCTGGACTGCTGTGTCGTGAGGACGGCTCTGGCGGTCACGACCGGCGGCTCGAGTCAAACAGTACAGGAGTCACGCTGGGGCGGTGGAACGCCGCTTCGGCAACGATCCGTCGTCTCCAGTCGAGAGGCGAATAAGCGTTATGCCGGGCGAAAAGTTGCCCGGTGTTGGAACCGAAGAACACGGCGGTGCGGAGTCCGGCGAGTAACGGAATACAAGCTTCGTGAGTAAACGATAAAGCGTGACTACATCAGTATCATGCCCAACCAGACGGGTTAACGGCACAAAGACACGCGAGAGGACGTTCGAGCATTATAACGAATGGCACGCATAGTACGCTGGGTTATCGCTCGCCACGTATCGCGGCAGCGGCTAGTAAGTGGGTTAAGTGATGACAACAGATTGGAATATAGAGGAACCCGGTTCTTGTCCCATGATGTTCAAACTTGTCAATATCCTGC $ cat 13183.fasta U00096.3_3945588_aligned_2 TACTAGGAGCAGCCCCCCTCAGTCTCCAGCGCCCACGCAAGGGACCGAACTTGTCCGTGTTCTAAACCCAGCTCGCGTACCATTGTAAATGCGAAGACAATACCCTTGGGACCTACTTCAGCTCCAGGATGTGATGCGGACATCGCGCCAAACACCACCGTCTATATTTACTCTTGGGCGGATCAGCCTGTTATCCGGAGTACCTATCCGTTGATCGGCCCTGCATTCAGAACCCCGGATCACTATGACCTGCTTTCGCACCTGCCTCGCCGTCACGCTGCAGTCAAGCTGGCTTATGCCATTAGCACTAACCTCCTGATGTCCGACCCAGGATTAGCCAACCTTCGTGCTCCTCCGTTACTGAGGACCGCCCCAGTCAATCTACCCACCAGTACACTGTCCGCAACGACCGGGACCACGTGTATAGAACATAAACAACATAAAGGAAAGTATTTCAAGGTCGGCTCCATGCAGACTGTACCACACTTCAAAGCCTCTCTATCCTACACTCAAGGCTCAATGTTCAGTGTCAAGCGTATAGTAAAGCTTCACGGGGCCTTTCTATCGGCGGGTACACTCCATCTTCACATGCGCAGTTCAATTTCACTGAGTCTCGGGTGCGAGACAGCCTGGCCTCCGCCATTCGTGCAGACTTAGCCGACAAGGAATTTCGCCCTTAGACCGTAATACACGGCCGCCGTGTACGTTCGCGGGGCTTCGA
If I remove the 1st nt from the first sequence, 2158.fasta, the alignment finishes successfully. If I remove the 2nd nt from the second sequence, 13183.fasta, the alignment finishes successfully as well. Otherwise, they throw the "glibc" error. I used gcc/7.1, but the error occurred with older gcc versions too.
I hope this helps, and please let me know if you need any additional information.
Thank you, Natasha
ocxtal
commented
6 years ago Fixed at 24776ca. It was a buffer overrun error which breaks glibc memory management data structure.
The sequences resulted in the following alignments. I would appreciate if you test the updated master branch and check if it runs properly.
@HD VN:1.0 SO:unsorted
@SQ SN:gi|556503834|ref|NC_000913.3| LN:4641652
@PG ID:minialign PN:minialign VN:0.6.0-12-g6f04aaf CL:/home/suzukihajime/docs/src/minialign/minialign -x ont.r9.1d -O sam -T MD,AS,NM index.2.mai npavlovikj.fa
U00096.3_1467868_aligned_1 16 gi|556503834|ref|NC_000913.3| 1467869 40 13M1I2M1D22M1D2M1D2M1D3M1D8M1D4M2D1M1D5M1I1M1I1M1I13M1I7M1D10M1D4M4D30M1D1M1D25M1I5M1I2M3D2M1I6M1D18M1D37M2I8M2D2M1D2M1D42M1D1M4D1M1D6M1D6M1D2M4D1M1D1M1D4M4D4M1D1M2D4M1D3M1I1M1D4M3D2M1D20M1D1M2D28M1D11M1D16M2D3M1D18M1D10M1D8M1D16M1I4M2D1M1D3M2I2M1I2M1D3M1I10M2D64M1I2M1D11M1D8M2D1M1D15M1D12M1D1M1D2M1D2M1I16M2D1M1D53M2I1M2D16M2D1M1D1M1D16M1D3M2D14M1D11M2D16M1I6M1D4M2D11M1D22M1D1M1D17M1D16M1D87M1I21M2D12M2D17M1I2M4D2M1D2M1I3M1I3M2I2M3I8M1D8M1D4M1D7M2I3M2D4M3D2M1D5M1I16M1D9M1I1M2D4M1D16M1D2M1D7M1D4M1I6M2D13M1D5M2D66M1I2M1D14M2D6M1D1M1D49M * 0 0 GCAGGATATTGACAAGTTTGAACATCATGGGACAAGAACCGGGTTCCTCTATATTCCAATCTGTTGTCATCACTTAACCCACTTACTAGCCGCTGCCGCGATACGTGGCGAGCGATAACCCAGCGTACTATGCGTGCCATTCGTTATAATGCTCGAACGTCCTCTCGCGTGTCTTTGTGCCGTTAACCCGTCTGGTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTACTCACGAAGCTTGTATTCCGTTACTCGCCGGACTCCGCACCGCCGTGTTCTTCGGTTCCAACACCGGGCAACTTTTCGCCCGGCATAACGCTTATTCGCCTCTCGACTGGAGACGACGGATCGTTGCCGAAGCGGCGTTCCACCGCCCCAGCGTGACTCCTGTACTGTTTGACTCGAGCCGCCGGTCGTGACCGCCAGAGCCGTCCTCACGACACAGCAGTCCAGCGCGGAACGCACTTTCAAGCTCGTCTCCGTTATCAGCAGAACTCGAACCCGTCAGAGCACCATCGCTGATTGCTTTCTTTCACGGCCACTCTGCCTGCCACTGCCCGTTTCATTGCGGTACAGGTTTTCGCTCAACAACAGCGCATTTGCCAGTGATCCGGTAAATGCGTGCATTGATCGCAGGCATACCATCAAGTTCTGCCTGTCTGCGAAGCAGCGCCCAGGTTTGACGATAACCATACTGAGCTCTCCGATATCATATGGACGGAGAAGCACACCGTATCATCAGTGACGACTGCTCCGGACCAGCCTCCACATCGGTTCGTGGAGAATGACGTGCAACTGCGCCCGACACCCGGAGAAAACGCTGACTAAGCTTACTCCCATCCCCGGGCAATAAGGGCGCGGGCGCTATCCACTTTTTTGCCCGTCCATATTCAACGGCTTCTTTGAGGAGTTCATTTTCCATACGTTTTCTTGCCGAGCAGACGGGAGTTGTTTAAGGCTTCATGGCGGCAGCGAAAGGGACCGCCAACTCATCTGCCTGTTCCCGGCGGCACAGAGTAAAATGCTTTTCCTAGGCTTCACGCCAGAGAAATAACAGCTGGCTGACCACCTGTCGCCGGGCAACGAGGGACAGTCTCCCAGGGTTCAGCTCTGCTGAACATTGCTCTTTTCCTGTGCAGTACGCTGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATTGCTAGTCTATAAACTTAGTAAATATCACTTATTTAAGTGATATTGGGGGTCTGGAGATTCAGGGGGCCAGT * AS:i:2785 NM:i:235 MD:Z:15^T22^C2^T2^A0T2^G2C5^T4^AG1^C24A2^C10^A4^TTCC22C7^G1^A32^AAG8^C18^T45^CT2^C2^C13T28^T1^CAAG1^C6^T6^G2^CTGG1^G1^G4^ATTA4^G1^TA4^G4^A4^CCG2^A3A3C12^G1^AA28^T6A4^G13C2^TG1T1^A10A7^C4T2A2^G8^T20^GT1^A3G3^T13^CA64T1^T0G10^G2G5^AC1^G15^G12^C1^G2^G14C0A2^TT1^G54^AC0C0C14^GT1^G1^C12A3^G0G2^TA0T13^T11^GT11G0G6T2^A4^GT11^C0T21^A1^G13C3^G16^C25T79G2^CT6C5^TC0T18^GTTC2^A3A1G4A7^T8^G4^C5G4^CC4^TGG2^T0T20^T0G9^TA4^A3T12^G2^A3C3^A4C5^AA13^A5^GA12T0G6C47^A8A5^AG2T3^G1^C24T0T23
U00096.3_1467868_aligned_1 256 gi|556503834|ref|NC_000913.3| 3186099 0 49M1D1M1D6M2D14M1D1M1I67M2D4M1D13M2D4M1I7M1D3M2D22M1D3M1I2M2D7M1D18M1I4M4D7M2D3M2I7M1D4M1D8M1D5M1I1M2I1M1I1M1I4M1I4M1I2M1D2M4D2M1I16M2D13M2D21M1I84M1D18M1D18M1D1M1D21M1D12M2D4M1D6M1I13M2D14M1D12M2D4M1D17M2D1M1D1M1D14M2D3M2I52M1D1M2D17M1I2M1D1M1D2M1D12M1D11M1D1M2D12M1D10M1D2M1I63M2D12M1I3M1D1M1I2M2I4M3D4M1I17M1D8M1D8M1D19M1D2M2D18M1D11M1D26M3D23M1D2M3D4M1D1M1I3M1D3M3D6M4D1M1D2M1D1M4D4M1D6M1D4M2D1M4D45M1D1M2D1M1D10M2I35M1D20M1D5M1D2M1I1M2D2M1I5M1I25M2D30M2D1M2D4M1D8M1D9M1I13M3I6M2D1M1D3M1D10M2D9M36H * 0 0 ACTGGCCCCCTGAATCTCCAGACCCCCAATATCACTTAAATAAGTGATATTTACTAAGTTTATAGACTAGCAATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACAGCGTACTGCACAGGAAAAGAGCAATGTTCAGCAGAGCTGAACCCTGGGAGACTGTCCCTCGTTGCCCGGCGACAGGTGGTCAGCCAGCTGTTATTTCTCTGGCGTGAAGCCTAGGAAAAGCATTTTACTCTGTGCCGCCGGGAACAGGCAGATGAGTTGGCGGTCCCTTTCGCTGCCGCCATGAAGCCTTAAACAACTCCCGTCTGCTCGGCAAGAAAACGTATGGAAAATGAACTCCTCAAAGAAGCCGTTGAATATGGACGGGCAAAAAAGTGGATAGCGCCCGCGCCCTTATTGCCCGGGGATGGGAGTAAGCTTAGTCAGCGTTTTCTCCGGGTGTCGGGCGCAGTTGCACGTCATTCTCCACGAACCGATGTGGAGGCTGGTCCGGAGCAGTCGTCACTGATGATACGGTGTGCTTCTCCGTCCATATGATATCGGAGAGCTCAGTATGGTTATCGTCAAACCTGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCACGCATTTACCGGATCACTGGCAAATGCGCTGTTGTTGAGCGAAAACCTGTACCGCAATGAAACGGGCAGTGGCAGGCAGAGTGGCCGTGAAAGAAAGCAATCAGCGATGGTGCTCTGACGGGTTCGAGTTCTGCTGATAACGGAGACGAGCTTGAAAGTGCGTTCCGCGCTGGACTGCTGTGTCGTGAGGACGGCTCTGGCGGTCACGACCGGCGGCTCGAGTCAAACAGTACAGGAGTCACGCTGGGGCGGTGGAACGCCGCTTCGGCAACGATCCGTCGTCTCCAGTCGAGAGGCGAATAAGCGTTATGCCGGGCGAAAAGTTGCCCGGTGTTGGAACCGAAGAACACGGCGGTGCGGAGTCCGGCGAGTAACGGAATACAAGCTTCGTGAGTAAACGATAAAGCGTGACTACATCAGTATCATGCCCAACCAGACGGGTTAACGGCACAAAGACACGCGAGAGGACGTTCGAGCATTATAACGAATGGCACGCATAGTACGCTGGGTTATCGCTCGCCACGTATCGCGGCAGCGGCTAGTAAGTGGGTTAAGTGATGACAACAGATTGGAATATAGAGGAACCCGGTT * AS:i:2684 NM:i:232 MD:Z:23A0A24^G1^C3A2^CT5T8^T47G6C0A12^TC4^T13^TT6G4^T3^GG1C16A3^T5^AG7^C1A20^AATA1C5^GG4C5^G4^C8^A8T3C1T3^T2^GAAC18^AG0A5G6^AG2C79A22^G18^C4G13^C1^T21^A0G11^AC4^T2A6C0C8^CA14^A12^TA1A2^C0C3T12^GC1^A1^C14^GG0G0T53^C1^AA3T0G14^C1^C2^G12^C11^C1^TG9C2^C10^C0A1A62^TG15^A3C3^TCA21^A8^C2T2A2^G9T9^T2^AA0C3G13^C4T6^A26^TCT15G3T3^T2^CGG4^T4^C3^CTA6^TAAT1^A2^C1^CGCC4^C6^A4^GG1^ACTT31A13^G1^AG1^G45^A20^G5^A3^TT32^TC8G21^GG1^AA4^T8^G4T23^TG1^C3^A7G2^CA2T2A3
U00096.3_1467868_aligned_1 256 gi|556503834|ref|NC_000913.3| 381263 0 49M1D1M1D6M2D14M1D1M1I67M2D4M1D13M2D4M1I7M1D3M2D22M1D3M1I2M2D7M1D18M1I4M4D7M2D3M2I7M1D4M1D8M1D5M1I1M2I1M1I1M1I4M1I4M1I2M1D2M4D2M1I16M2D13M2D21M1I84M1D18M1D18M1D1M1D21M1D12M2D4M1D6M1I13M2D14M1D12M2D4M1D17M2D1M1D1M1D14M2D3M2I52M1D1M2D17M1I2M1D1M1D2M1D12M1D11M1D1M2D12M1D10M1D2M1I63M2D12M1I3M1D1M1I2M2I4M3D4M1I17M1D8M1D8M1D19M1D2M2D18M1D11M1D26M3D23M1D2M3D4M1D1M1I3M1D3M3D6M4D1M1D2M1D1M4D4M1D6M1D4M2D1M4D45M1D1M2D1M1D10M2I35M1D20M1D5M1D2M1I1M2D2M1I5M1I25M2D30M2D1M2D4M1D8M1D9M1I13M3I6M2D1M1D3M1D10M1D2M43H * 0 0 ACTGGCCCCCTGAATCTCCAGACCCCCAATATCACTTAAATAAGTGATATTTACTAAGTTTATAGACTAGCAATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACAGCGTACTGCACAGGAAAAGAGCAATGTTCAGCAGAGCTGAACCCTGGGAGACTGTCCCTCGTTGCCCGGCGACAGGTGGTCAGCCAGCTGTTATTTCTCTGGCGTGAAGCCTAGGAAAAGCATTTTACTCTGTGCCGCCGGGAACAGGCAGATGAGTTGGCGGTCCCTTTCGCTGCCGCCATGAAGCCTTAAACAACTCCCGTCTGCTCGGCAAGAAAACGTATGGAAAATGAACTCCTCAAAGAAGCCGTTGAATATGGACGGGCAAAAAAGTGGATAGCGCCCGCGCCCTTATTGCCCGGGGATGGGAGTAAGCTTAGTCAGCGTTTTCTCCGGGTGTCGGGCGCAGTTGCACGTCATTCTCCACGAACCGATGTGGAGGCTGGTCCGGAGCAGTCGTCACTGATGATACGGTGTGCTTCTCCGTCCATATGATATCGGAGAGCTCAGTATGGTTATCGTCAAACCTGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCACGCATTTACCGGATCACTGGCAAATGCGCTGTTGTTGAGCGAAAACCTGTACCGCAATGAAACGGGCAGTGGCAGGCAGAGTGGCCGTGAAAGAAAGCAATCAGCGATGGTGCTCTGACGGGTTCGAGTTCTGCTGATAACGGAGACGAGCTTGAAAGTGCGTTCCGCGCTGGACTGCTGTGTCGTGAGGACGGCTCTGGCGGTCACGACCGGCGGCTCGAGTCAAACAGTACAGGAGTCACGCTGGGGCGGTGGAACGCCGCTTCGGCAACGATCCGTCGTCTCCAGTCGAGAGGCGAATAAGCGTTATGCCGGGCGAAAAGTTGCCCGGTGTTGGAACCGAAGAACACGGCGGTGCGGAGTCCGGCGAGTAACGGAATACAAGCTTCGTGAGTAAACGATAAAGCGTGACTACATCAGTATCATGCCCAACCAGACGGGTTAACGGCACAAAGACACGCGAGAGGACGTTCGAGCATTATAACGAATGGCACGCATAGTACGCTGGGTTATCGCTCGCCACGTATCGCGGCAGCGGCTAGTAAGTGGGTTAAGTGATGACAACAGATTGGAATATAGAGGAA * AS:i:2682 NM:i:229 MD:Z:23A0A24^G1^C3A2^CT5T8^T47G6C0A12^TC4^T13^TT6G4^T3^GG1C16A3^T5^AG7^C1A20^AATA1C5^GG4C5^G4^C8^A8T3C1T3^T2^GAAC18^AG0A5G6^AG2C79A22^G18^C4G13^C1^T21^A0G11^AC4^T2A6C0C8^CA14^A12^TA1A2^C0C3T12^GC1^A1^C14^GG0G0T53^C1^AA3T0G14^C1^C2^G12^C11^C1^TG9C2^C10^C0A1A62^TG15^A3C3^TCA21^A8^C2T2A2^G9T9^T2^AA0C3G13^C4T6^A26^TCT15G3T3^T2^CGG4^T4^C3^CTA6^TAAT1^A2^C1^CGCC4^C6^A4^GG1^ACTT31A13^G1^AG1^G45^A20^G5^A3^TT32^TC8G21^GG1^AA4^T8^G4T23^TG1^C3^A7G2^C2
U00096.3_1467868_aligned_1 272 gi|556503834|ref|NC_000913.3| 2068946 0 43H2M1D8M1D4M2D1M1D5M1I1M1I1M1I13M1I7M1D10M1D4M4D30M1D1M1D25M1I5M1I2M3D2M1I6M1D18M1D37M2I8M2D2M1D2M1D42M1D1M4D1M1D6M1D6M1D2M4D1M1D1M1D4M4D4M1D1M2D4M1D3M1I1M1D4M3D2M1D20M1D1M2D28M1D11M1D16M2D3M1D18M1D10M1D8M1D16M1I4M2D1M1D3M2I2M1I2M1D3M1I10M2D64M1I2M1D11M1D8M2D1M1D15M1D12M1D1M1D2M1D2M1I16M2D1M1D53M2I1M2D16M2D1M1D1M1D16M1D3M2D14M1D11M2D16M1I6M1D4M2D11M1D22M1D1M1D17M1D16M1D87M1I21M2D12M2D17M1I2M4D2M1D2M1I3M1I3M2I2M3I8M1D8M1D4M1D7M2I3M2D4M3D2M1D5M1I16M1D9M1I1M2D4M1D16M1D2M1D7M1D4M1I6M2D13M1D5M2D66M1I2M1D14M2D6M1D1M1D49M * 0 0 TTCCTCTATATTCCAATCTGTTGTCATCACTTAACCCACTTACTAGCCGCTGCCGCGATACGTGGCGAGCGATAACCCAGCGTACTATGCGTGCCATTCGTTATAATGCTCGAACGTCCTCTCGCGTGTCTTTGTGCCGTTAACCCGTCTGGTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTACTCACGAAGCTTGTATTCCGTTACTCGCCGGACTCCGCACCGCCGTGTTCTTCGGTTCCAACACCGGGCAACTTTTCGCCCGGCATAACGCTTATTCGCCTCTCGACTGGAGACGACGGATCGTTGCCGAAGCGGCGTTCCACCGCCCCAGCGTGACTCCTGTACTGTTTGACTCGAGCCGCCGGTCGTGACCGCCAGAGCCGTCCTCACGACACAGCAGTCCAGCGCGGAACGCACTTTCAAGCTCGTCTCCGTTATCAGCAGAACTCGAACCCGTCAGAGCACCATCGCTGATTGCTTTCTTTCACGGCCACTCTGCCTGCCACTGCCCGTTTCATTGCGGTACAGGTTTTCGCTCAACAACAGCGCATTTGCCAGTGATCCGGTAAATGCGTGCATTGATCGCAGGCATACCATCAAGTTCTGCCTGTCTGCGAAGCAGCGCCCAGGTTTGACGATAACCATACTGAGCTCTCCGATATCATATGGACGGAGAAGCACACCGTATCATCAGTGACGACTGCTCCGGACCAGCCTCCACATCGGTTCGTGGAGAATGACGTGCAACTGCGCCCGACACCCGGAGAAAACGCTGACTAAGCTTACTCCCATCCCCGGGCAATAAGGGCGCGGGCGCTATCCACTTTTTTGCCCGTCCATATTCAACGGCTTCTTTGAGGAGTTCATTTTCCATACGTTTTCTTGCCGAGCAGACGGGAGTTGTTTAAGGCTTCATGGCGGCAGCGAAAGGGACCGCCAACTCATCTGCCTGTTCCCGGCGGCACAGAGTAAAATGCTTTTCCTAGGCTTCACGCCAGAGAAATAACAGCTGGCTGACCACCTGTCGCCGGGCAACGAGGGACAGTCTCCCAGGGTTCAGCTCTGCTGAACATTGCTCTTTTCCTGTGCAGTACGCTGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATTGCTAGTCTATAAACTTAGTAAATATCACTTATTTAAGTGATATTGGGGGTCTGGAGATTCAGGGGGCCAGT * AS:i:2682 NM:i:229 MD:Z:0T0T0^G0C0C0C0C3A0^T0T0T1C0^AG1^C0A1C2T0T0A0T0C0A0C0T0T0A1C0C0C1T0T0A0C0A0A0G0^C1C0G0C0T0G0C0C0G1^A0G1T0A0^TTCC1G0T0G0G0C0G0A0G0C0G1T0A0A0C0C1A0G0C0G0C0A0C0T0A0T2^G0G0^A0T0G0C0C0A0T0T2T2T0A0A0T2T0C1A0A0C0G0C1T1T0G0C0^AAG0G0T1C1T0T1^C4G2A0A0C0C0C0G0T0C2G0^T1T1G0G1A1G0A1A0C0T1A0T0G0T0A0G1C0A0C0G0C0T0T0T0A1C0G0T0T0T0T0C0A0C0G0A0A1^CT0C0T0^C0T0G0^C0T2T1C1T1A0C0T0C2C0G1A0C1C0C0G1A0C0C0G0C1G0T0G0T0T0C0T0T1G0G0^T0T0^CAAG1^C0C0C0A0A1A0^T0C0C0G0G0G1^G0A0A0^CTGG1^G0T0^G0T0T0T0C0^ATTA0G1C1^G0G0^TA0G1A0T0^G0A0A0C0C0^A1T0A1^CCG0T0C0^A1C0C0A1T0C3T2A0G1C0G0A0C0^G0G0^AA0G0A0T1G0T0T2C0G2G0C0G0G0C0G3C0A1C0G0C0^T1C0C0A0G0C0A0T3^G0T0C1T1T0A1T0G1T0T1A0C0^TG0T0T0G0^A0A2C0G0C1G0G0T0A1T0G0A1C1^C1C0A1T0G0C0A0G1^G0C0C0T1A0C0G0A0^T0C0A0C0A0G1A0G0T2A0G2C0G0A0A0C0^GT0G0^A1A0C0G0C0A0G0^T1T0C0T0C0T0C2T0T1T0^CA0C0A0G0C0A0G0A0A0C0T2A0A0C0C0C0G0T2G0A0G0C0A0C0C0A0T0C0G0C1G0A0T0T1C1T2T0T0T0C0A0C0G0G0C1A0C0T1T0G0C0C0T0G0T0A0^T0G0T0G1C0C0G0T0T1C0^G2G2G0G1^AC0A0^G0C0A0G0G0T0T0T0T1G0C0T0C0A0A0^G0C0A0A0C0A0G1G1A0T0T0^C0T0^G0G0C0^G0C0A0T0G0A1C5A1C0A0C0G0^TT1^G0G1A0T1G1T1G0C0A0G2A0T1C0C0A0T1A3T0C1G1C0T0G0T0C0T0G0C0G0A0A3G0C1C0C1A0T0^AC0C1G0A0C0G0A0T0A0A0C0C0A1A1^GT1^G1^C0A0G0C0T0C0T0C0C0G0A0T1A2T0^G0G0T0G0^TA0T0A0C2A0G0A0A0G1A0C0A0^T0C0C0G0T2C0A1C1^GT1T0G0A0C0G0A0C0T0G0C0G0G0C0G0G0C0C1T0C0C0^A0T0C0C1^GT0C0A0T1G0G0T0T0C0G1^C0T0G0A0G1A5T0G0C0A0A0C0T0G0C1C0^A1^G1G0A1A0C2G0G1G0A0C0A0A0C0^G0G0C2A0C0T2G0C0T0T0A0C0T0^C1C0C0A1C1C1G0G1C0A1T0A0A2G0C0G0C0G0T0G0C0G0C0T1T0C0C1C0T2T0T1G2C0G0T2A0T0A0T0T0C1A0C0G1C0T0T0C0T0T0T1A1G0A0G1T2T3C0C0A0T1G0T1T0T0C1T0G0C1G1G0C0A0G0G0C0G0^CT0G0G0A1T0T0C0T0T1A0A0^TC0T0G0C3A0T0G0G2G0C0A0G1A0A0^GTTC0A0G0^A1G3G0A0A0C0A0A0C0C0T1T0T0C0^T0C1G0G0C1G0C0^G0A3^C0A1T3A1T0T0^CC0T0T0C0C0^TGG0T0A0^T0T0G0C0T1A1G0C0C0A0G0A0G0A0A0A0T0A0A0C0^T0G0G0C0T1G0C0T0G0C0^TA0C0A0C0C0^A1G0T0T0G0C0C1G0G0C0A3A0^G0G0G0^A2C0C0G0T0C0^A0T0C1C1G1T0T0C0^AA0A0G1T0C0T0G0C0T0G0A0A1^A0A0T0T2^GA0T0C0T0T0T0T0C0C0T0G0T2G0G0T0A1G0C0C2C0T0G0C0G1T1C0T0C0C0G0G1C0C1A0A0G0A0C0A1C0A0A1C0A0T1T2T1T1C0A0A2^A1T0A0G3A0A0A0A0A1T0^AG2T0T1A0^G1^C1A0T0C0A1T1A1T1A0A0G0T0G1T0A1T0G0G0T0T0G0T0C0T0G0G1G0A2C0A0G0G0G0G0G0C0C0A0G0T0
U00096.3_1467868_aligned_1 272 gi|556503834|ref|NC_000913.3| 2996366 0 43H2M1D8M1D4M2D1M1D5M1I1M1I1M1I13M1I7M1D10M1D4M4D30M1D1M1D25M1I5M1I2M3D2M1I6M1D18M1D37M2I8M2D2M1D2M1D42M1D1M4D1M1D6M1D6M1D2M4D1M1D1M1D4M4D4M1D1M2D4M1D3M1I1M1D4M3D2M1D20M1D1M2D28M1D11M1D16M2D3M1D18M1D10M1D8M1D16M1I4M2D1M1D3M2I2M1I2M1D3M1I10M2D64M1I2M1D11M1D8M2D1M1D15M1D12M1D1M1D2M1D2M1I16M2D1M1D53M2I1M2D16M2D1M1D1M1D16M1D3M2D14M1D11M2D16M1I6M1D4M2D11M1D22M1D1M1D17M1D16M1D87M1I21M2D12M2D17M1I2M4D2M1D2M1I3M1I3M2I2M3I8M1D8M1D4M1D7M2I3M2D4M3D2M1D5M1I16M1D9M1I1M2D4M1D16M1D2M1D7M1D4M1I6M2D13M1D5M2D66M1I2M1D14M2D6M1D1M1D49M * 0 0 TTCCTCTATATTCCAATCTGTTGTCATCACTTAACCCACTTACTAGCCGCTGCCGCGATACGTGGCGAGCGATAACCCAGCGTACTATGCGTGCCATTCGTTATAATGCTCGAACGTCCTCTCGCGTGTCTTTGTGCCGTTAACCCGTCTGGTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTACTCACGAAGCTTGTATTCCGTTACTCGCCGGACTCCGCACCGCCGTGTTCTTCGGTTCCAACACCGGGCAACTTTTCGCCCGGCATAACGCTTATTCGCCTCTCGACTGGAGACGACGGATCGTTGCCGAAGCGGCGTTCCACCGCCCCAGCGTGACTCCTGTACTGTTTGACTCGAGCCGCCGGTCGTGACCGCCAGAGCCGTCCTCACGACACAGCAGTCCAGCGCGGAACGCACTTTCAAGCTCGTCTCCGTTATCAGCAGAACTCGAACCCGTCAGAGCACCATCGCTGATTGCTTTCTTTCACGGCCACTCTGCCTGCCACTGCCCGTTTCATTGCGGTACAGGTTTTCGCTCAACAACAGCGCATTTGCCAGTGATCCGGTAAATGCGTGCATTGATCGCAGGCATACCATCAAGTTCTGCCTGTCTGCGAAGCAGCGCCCAGGTTTGACGATAACCATACTGAGCTCTCCGATATCATATGGACGGAGAAGCACACCGTATCATCAGTGACGACTGCTCCGGACCAGCCTCCACATCGGTTCGTGGAGAATGACGTGCAACTGCGCCCGACACCCGGAGAAAACGCTGACTAAGCTTACTCCCATCCCCGGGCAATAAGGGCGCGGGCGCTATCCACTTTTTTGCCCGTCCATATTCAACGGCTTCTTTGAGGAGTTCATTTTCCATACGTTTTCTTGCCGAGCAGACGGGAGTTGTTTAAGGCTTCATGGCGGCAGCGAAAGGGACCGCCAACTCATCTGCCTGTTCCCGGCGGCACAGAGTAAAATGCTTTTCCTAGGCTTCACGCCAGAGAAATAACAGCTGGCTGACCACCTGTCGCCGGGCAACGAGGGACAGTCTCCCAGGGTTCAGCTCTGCTGAACATTGCTCTTTTCCTGTGCAGTACGCTGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATTGCTAGTCTATAAACTTAGTAAATATCACTTATTTAAGTGATATTGGGGGTCTGGAGATTCAGGGGGCCAGT * AS:i:2682 NM:i:229 MD:Z:0T0T0^G0C0C0C0C3A0^T0T0T1C0^AG1^C0A1C2T0T0A0T0C0A0C0T0T0A1C0C0C1T0T0A0C0A0A0G0^C1C0G0C0T0G0C0C0G1^A0G1T0A0^TTCC1G0T0G0G0C0G0A0G0C0G1T0A0A0C0C1A0G0C0G0C0A0C0T0A0T2^G0G0^A0T0G0C0C0A0T0T2T2T0A0A0T2T0C1A0A0C0G0C1T1T0G0C0^AAG0G0T1C1T0T1^C4G2A0A0C0C0C0G0T0C2G0^T1T1G0G1A1G0A1A0C0T1A0T0G0T0A0G1C0A0C0G0C0T0T0T0A1C0G0T0T0T0T0C0A0C0G0A0A1^CT0C0T0^C0T0G0^C0T2T1C1T1A0C0T0C2C0G1A0C1C0C0G1A0C0C0G0C1G0T0G0T0T0C0T0T1G0G0^T0T0^CAAG1^C0C0C0A0A1A0^T0C0C0G0G0G1^G0A0A0^CTGG1^G0T0^G0T0T0T0C0^ATTA0G1C1^G0G0^TA0G1A0T0^G0A0A0C0C0^A1T0A1^CCG0T0C0^A1C0C0A1T0C3T2A0G1C0G0A0C0^G0G0^AA0G0A0T1G0T0T2C0G2G0C0G0G0C0G3C0A1C0G0C0^T1C0C0A0G0C0A0T3^G0T0C1T1T0A1T0G1T0T1A0C0^TG0T0T0G0^A0A2C0G0C1G0G0T0A1T0G0A1C1^C1C0A1T0G0C0A0G1^G0C0C0T1A0C0G0A0^T0C0A0C0A0G1A0G0T2A0G2C0G0A0A0C0^GT0G0^A1A0C0G0C0A0G0^T1T0C0T0C0T0C2T0T1T0^CA0C0A0G0C0A0G0A0A0C0T2A0A0C0C0C0G0T2G0A0G0C0A0C0C0A0T0C0G0C1G0A0T0T1C1T2T0T0T0C0A0C0G0G0C1A0C0T1T0G0C0C0T0G0T0A0^T0G0T0G1C0C0G0T0T1C0^G2G2G0G1^AC0A0^G0C0A0G0G0T0T0T0T1G0C0T0C0A0A0^G0C0A0A0C0A0G1G1A0T0T0^C0T0^G0G0C0^G0C0A0T0G0A1C5A1C0A0C0G0^TT1^G0G1A0T1G1T1G0C0A0G2A0T1C0C0A0T1A3T0C1G1C0T0G0T0C0T0G0C0G0A0A3G0C1C0C1A0T0^AC0C1G0A0C0G0A0T0A0A0C0C0A1A1^GT1^G1^C0A0G0C0T0C0T0C0C0G0A0T1A2T0^G0G0T0G0^TA0T0A0C2A0G0A0A0G1A0C0A0^T0C0C0G0T2C0A1C1^GT1T0G0A0C0G0A0C0T0G0C0G0G0C0G0G0C0C1T0C0C0^A0T0C0C1^GT0C0A0T1G0G0T0T0C0G1^C0T0G0A0G1A5T0G0C0A0A0C0T0G0C1C0^A1^G1G0A1A0C2G0G1G0A0C0A0A0C0^G0G0C2A0C0T2G0C0T0T0A0C0T0^C1C0C0A1C1C1G0G1C0A1T0A0A2G0C0G0C0G0T0G0C0G0C0T1T0C0C1C0T2T0T1G2C0G0T2A0T0A0T0T0C1A0C0G1C0T0T0C0T0T0T1A1G0A0G1T2T3C0C0A0T1G0T1T0T0C1T0G0C1G1G0C0A0G0G0C0G0^CT0G0G0A1T0T0C0T0T1A0A0^TC0T0G0C3A0T0G0G2G0C0A0G1A0A0^GTTC0A0G0^A1G3G0A0A0C0A0A0C0C0T1T0T0C0^T0C1G0G0C1G0C0^G0A3^C0A1T3A1T0T0^CC0T0T0C0C0^TGG0T0A0^T0T0G0C0T1A1G0C0C0A0G0A0G0A0A0A0T0A0A0C0^T0G0G0C0T1G0C0T0G0C0^TA0C0A0C0C0^A1G0T0T0G0C0C1G0G0C0A3A0^G0G0G0^A2C0C0G0T0C0^A0T0C1C1G1T0T0C0^AA0A0G1T0C0T0G0C0T0G0A0A1^A0A0T0T2^GA0T0C0T0T0T0T0C0C0T0G0T2G0G0T0A1G0C0C2C0T0G0C0G1T1C0T0C0C0G0G1C0C1A0A0G0A0C0A1C0A0A1C0A0T1T2T1T1C0A0A2^A1T0A0G3A0A0A0A0A1T0^AG2T0T1A0^G1^C1A0T0C0A1T1A1T1A0A0G0T0G1T0A1T0G0G0T0T0G0T0C0T0G0G1G0A2C0A0G0G0G0G0G0C0C0A0G0T0
U00096.3_1467868_aligned_1 256 gi|556503834|ref|NC_000913.3| 1650845 0 587H52M1D1M2D17M1I2M1D1M1D2M1D12M1D11M1D1M2D12M1D10M1D2M1I63M2D12M1I3M1D1M1I2M2I4M3D4M1I17M1D8M1D8M1D19M1D2M2D18M1D11M1D26M3D23M1D2M3D4M1D1M1I3M1D3M3D6M4D1M1D2M1D1M4D4M1D6M1D4M2D1M4D45M1D1M2D1M1D10M2I35M1D20M1D5M1D2M1I1M2D2M1I5M1I25M2D30M2D1M2D4M1D8M1D9M1I13M3I6M2D1M1D3M1D10M2D2M1D2M1D1M1D3M2D3M1D2M1D3M1D1M1I2M1D5M3I2M2I1M1I5M6H * 0 0 TGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCACGCATTTACCGGATCACTGGCAAATGCGCTGTTGTTGAGCGAAAACCTGTACCGCAATGAAACGGGCAGTGGCAGGCAGAGTGGCCGTGAAAGAAAGCAATCAGCGATGGTGCTCTGACGGGTTCGAGTTCTGCTGATAACGGAGACGAGCTTGAAAGTGCGTTCCGCGCTGGACTGCTGTGTCGTGAGGACGGCTCTGGCGGTCACGACCGGCGGCTCGAGTCAAACAGTACAGGAGTCACGCTGGGGCGGTGGAACGCCGCTTCGGCAACGATCCGTCGTCTCCAGTCGAGAGGCGAATAAGCGTTATGCCGGGCGAAAAGTTGCCCGGTGTTGGAACCGAAGAACACGGCGGTGCGGAGTCCGGCGAGTAACGGAATACAAGCTTCGTGAGTAAACGATAAAGCGTGACTACATCAGTATCATGCCCAACCAGACGGGTTAACGGCACAAAGACACGCGAGAGGACGTTCGAGCATTATAACGAATGGCACGCATAGTACGCTGGGTTATCGCTCGCCACGTATCGCGGCAGCGGCTAGTAAGTGGGTTAAGTGATGACAACAGATTGGAATATAGAGGAACCCGGTTCTTGTCCCATGATGTTCAAACTTGTCAATA * AS:i:1449 NM:i:142 MD:Z:52^C1^AA3T0G14^C1^C2^G12^C11^C1^TG9C2^C10^C0A1A62^TG15^A3C3^TCA21^A8^C2T2A2^G9T9^T2^AA0C3G13^C4T6^A26^TCT15G3T3^T2^CGG4^T4^C3^CTA6^TAAT1^A2^C1^CGCC4^C6^A4^GG1^ACTT31A13^G1^AG1^G45^A20^G5^A3^TT32^TC8G21^GG1^AA4^T8^G4T23^TG1^C3^A7G2^CA2^T2^A1^A3^GA0A2^A0C1^C3^T3^T0T12
U00096.3_1467868_aligned_1 256 gi|556503834|ref|NC_000913.3| 4498184 0 49M1D1M1D6M2D14M1D1M1I67M2D4M1D13M2D4M1I7M1D3M2D22M1D3M1I2M2D7M1D18M1I4M4D7M2D3M2I7M1D4M1D8M1D5M1I1M2I1M1I1M1I4M1I4M1I2M1D2M4D2M1I16M2D13M2D21M1I84M1D18M1D18M1D1M1D21M1D12M2D4M1D6M1I13M2D14M1D12M2D4M1D17M2D1M1D1M1D14M2D3M2I52M1D1M2D17M1I2M1D1M1D2M1D12M1D11M1D1M2D12M1D10M1D2M1I63M2D12M1I3M1D1M1I2M2I4M3D4M1I17M1D8M1D8M1D19M1D2M2D18M1D11M1D26M3D23M1D2M3D4M1D1M1I3M1D3M3D6M4D1M1D2M1D1M4D4M1D6M1D4M2D1M4D45M1D1M2D1M1D10M2I35M1D20M1D5M1D2M1I1M2D2M1I5M1I25M2D30M2D1M2D4M1D8M1D9M1I13M3I6M2D1M1D3M1D10M2D2M1D2M1D1M4I5M1I2M1I4M23H * 0 0 ACTGGCCCCCTGAATCTCCAGACCCCCAATATCACTTAAATAAGTGATATTTACTAAGTTTATAGACTAGCAATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACAGCGTACTGCACAGGAAAAGAGCAATGTTCAGCAGAGCTGAACCCTGGGAGACTGTCCCTCGTTGCCCGGCGACAGGTGGTCAGCCAGCTGTTATTTCTCTGGCGTGAAGCCTAGGAAAAGCATTTTACTCTGTGCCGCCGGGAACAGGCAGATGAGTTGGCGGTCCCTTTCGCTGCCGCCATGAAGCCTTAAACAACTCCCGTCTGCTCGGCAAGAAAACGTATGGAAAATGAACTCCTCAAAGAAGCCGTTGAATATGGACGGGCAAAAAAGTGGATAGCGCCCGCGCCCTTATTGCCCGGGGATGGGAGTAAGCTTAGTCAGCGTTTTCTCCGGGTGTCGGGCGCAGTTGCACGTCATTCTCCACGAACCGATGTGGAGGCTGGTCCGGAGCAGTCGTCACTGATGATACGGTGTGCTTCTCCGTCCATATGATATCGGAGAGCTCAGTATGGTTATCGTCAAACCTGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCACGCATTTACCGGATCACTGGCAAATGCGCTGTTGTTGAGCGAAAACCTGTACCGCAATGAAACGGGCAGTGGCAGGCAGAGTGGCCGTGAAAGAAAGCAATCAGCGATGGTGCTCTGACGGGTTCGAGTTCTGCTGATAACGGAGACGAGCTTGAAAGTGCGTTCCGCGCTGGACTGCTGTGTCGTGAGGACGGCTCTGGCGGTCACGACCGGCGGCTCGAGTCAAACAGTACAGGAGTCACGCTGGGGCGGTGGAACGCCGCTTCGGCAACGATCCGTCGTCTCCAGTCGAGAGGCGAATAAGCGTTATGCCGGGCGAAAAGTTGCCCGGTGTTGGAACCGAAGAACACGGCGGTGCGGAGTCCGGCGAGTAACGGAATACAAGCTTCGTGAGTAAACGATAAAGCGTGACTACATCAGTATCATGCCCAACCAGACGGGTTAACGGCACAAAGACACGCGAGAGGACGTTCGAGCATTATAACGAATGGCACGCATAGTACGCTGGGTTATCGCTCGCCACGTATCGCGGCAGCGGCTAGTAAGTGGGTTAAGTGATGACAACAGATTGGAATATAGAGGAACCCGGTTCTTGTCCCATGAT * AS:i:2689 NM:i:241 MD:Z:23A0A24^G1^C3A2^CT5T8^T47G6C0A12^TC4^T13^TT6G4^T3^GG1C16A3^T5^AG7^C1A20^AATA1C5^GG4C5^G4^C8^A8T3C1T3^T2^GAAC18^AG0A5G6^AG2C79A22^G18^C4G13^C1^T21^A0G11^AC4^T2A6C0C8^CA14^A12^TA1A2^C0C3T12^GC1^A1^C14^GG0G0T53^C1^AA3T0G14^C1^C2^G12^C11^C1^TG9C2^C10^C0A1A62^TG15^A3C3^TCA21^A8^C2T2A2^G9T9^T2^AA0C3G13^C4T6^A26^TCT15G3T3^T2^CGG4^T4^C3^CTA6^TAAT1^A2^C1^CGCC4^C6^A4^GG1^ACTT31A13^G1^AG1^G45^A20^G5^A3^TT32^TC8G21^GG1^AA4^T8^G4T23^TG1^C3^A7G2^CA2^T2^A6G5
U00096.3_3945588_aligned_2 16 gi|556503834|ref|NC_000913.3| 3945589 26 6M1I3M1I2M3I15M2D10M1D6M2D22M1D1M5D14M4D2M1D14M1I26M1I3M1I22M2D1M2D30M1I26M1D10M3D19M1I1M3D37M1D3M1I1M1I9M2I2M1I11M1D1M1D1M1D1M2D14M1I25M2D4M1D1M5D33M1I24M1I24M1D14M1D31M1D10M1D6M1D1M2D12M3D9M2D15M1D34M3D9M2D41M1D6M1D6M1I2M1D24M1D3M1D4M1D11M2D1M1D2M1D14M1D23M * 0 0TCGAAGCCCCGCGAACGTACACGGCGGCCGTGTATTACGGTCTAAGGGCGAAATTCCTTGTCGGCTAAGTCTGCACGAATGGCGGAGGCCAGGCTGTCTCGCACCCGAGACTCAGTGAAATTGAACTGCGCATGTGAAGATGGAGTGTACCCGCCGATAGAAAGGCCCCGTGAAGCTTTACTATACGCTTGACACTGAACATTGAGCCTTGAGTGTAGGATAGAGAGGCTTTGAAGTGTGGTACAGTCTGCATGGAGCCGACCTTGAAATACTTTCCTTTATGTTGTTTATGTTCTATACACGTGGTCCCGGTCGTTGCGGACAGTGTACTGGTGGGTAGATTGACTGGGGCGGTCCTCAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGGTCGGACATCAGGAGGTTAGTGCTAATGGCATAAGCCAGCTTGACTGCAGCGTGACGGCGAGGCAGGTGCGAAAGCAGGTCATAGTGATCCGGGGTTCTGAATGCAGGGCCGATCAACGGATAGGTACTCCGGATAACAGGCTGATCCGCCCAAGAGTAAATATAGACGGTGGTGTTTGGCGCGATGTCCGCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATTGTCTTCGCATTTACAATGGTACGCGAGCTGGGTTTAGAACACGGACAAGTTCGGTCCCTTGCGTGGGCGCTGGAGACTGAGGGGGGCTGCTCCTAGTA * AS:i:1607 NM:i:125 MD:Z:14A11^AA0C3A5^C6^TA17G4^T1^CCGAC14^TAAT2^T53C11^GG1^AA2C0G5A9C36^T10^GGT1G18^CGC29C0A0C5^A6G14A4^T1^A1^C1^GG25T13^TC4^C1^TAAAG81^G12C1^A31^T10^G1A4^C1^AT2C9^AAA9^GG15^A12T0C4C5C9^CAC1T7^GG1T37G1^C1G4^C8^G24^G0T2^T2G1^C11^TA1^C2^C14^A23
U00096.3_3945588_aligned_2 256 gi|556503834|ref|NC_000913.3| 2726528 0 22M1D14M1D2M2D1M1D12M1D4M1D2M1D25M1D2M1I5M1D7M1D38M2D9M3D37M1D13M2D10M3D12M3D5M1D13M1D31M1D14M1D24M1I22M1I33M2D1M2D1M2D2M1D1M1D27M1I13M2D1M1D2M2D10M2I2M1I8M1I2M1I4M1D37M3D2M1I16M2D1M1D12M1D26M1I25M1D1M1D1M1D2M1D24M1I3M1I26M1I14M1D2M4D13M5D1M1D23M2D5M1D10M2D12M1I1M3I3M1I11M *0 0 TACTAGGAGCAGCCCCCCTCAGTCTCCAGCGCCCACGCAAGGGACCGAACTTGTCCGTGTTCTAAACCCAGCTCGCGTACCATTGTAAATGCGAAGACAATACCCTTGGGACCTACTTCAGCTCCAGGATGTGATGCGGACATCGCGCCAAACACCACCGTCTATATTTACTCTTGGGCGGATCAGCCTGTTATCCGGAGTACCTATCCGTTGATCGGCCCTGCATTCAGAACCCCGGATCACTATGACCTGCTTTCGCACCTGCCTCGCCGTCACGCTGCAGTCAAGCTGGCTTATGCCATTAGCACTAACCTCCTGATGTCCGACCCAGGATTAGCCAACCTTCGTGCTCCTCCGTTACTGAGGACCGCCCCAGTCAATCTACCCACCAGTACACTGTCCGCAACGACCGGGACCACGTGTATAGAACATAAACAACATAAAGGAAAGTATTTCAAGGTCGGCTCCATGCAGACTGTACCACACTTCAAAGCCTCTCTATCCTACACTCAAGGCTCAATGTTCAGTGTCAAGCGTATAGTAAAGCTTCACGGGGCCTTTCTATCGGCGGGTACACTCCATCTTCACATGCGCAGTTCAATTTCACTGAGTCTCGGGTGCGAGACAGCCTGGCCTCCGCCATTCGTGCAGACTTAGCCGACAAGGAATTTCGCCCTTAGACCGTAATACACGGCCGCCGTGTACGTTCGCGGGGCTTCGA * AS:i:1583 NM:i:128 MD:Z:22^T14^G2^AG1^T12^G1C2^A2^A0C24^C7^G5C1^G1C23C12^GA2C6^GAG1T10G5G4G0A12^T13^CC10^TTT10G1^GAT5^T1C11^A31^T1G12^C79^CT1^TT1^AG2^G1^A15A24^CC1^G2^TT0A4T1A12C5^T6G0T0G28^GGC18^CC1^A0C11^A36G9T4^C1^G1^C0T1^G1C11G53^A2^ATTA13^GGTCG1^A5C17^TA5^G6T3^GT0T13A12
U00096.3_3945588_aligned_2 272 gi|556503834|ref|NC_000913.3| 4039405 0 6M1I3M1I2M3I15M2D10M1D6M2D22M1D1M5D14M4D2M1D14M1I26M1I3M1I22M2D1M2D30M1I26M1D10M3D19M1I1M3D37M1D3M1I1M1I9M2I2M1I11M2D2M1D1M2D14M1I25M2D4M1D1M5D33M1I24M1I24M1D14M1D31M1D10M1D6M1D1M2D12M3D9M2D15M1D34M3D9M2D41M1D6M1D6M1I2M1D24M1D3M1D4M1D11M2D1M1D2M1D14M1D23M * 0 0 TCGAAGCCCCGCGAACGTACACGGCGGCCGTGTATTACGGTCTAAGGGCGAAATTCCTTGTCGGCTAAGTCTGCACGAATGGCGGAGGCCAGGCTGTCTCGCACCCGAGACTCAGTGAAATTGAACTGCGCATGTGAAGATGGAGTGTACCCGCCGATAGAAAGGCCCCGTGAAGCTTTACTATACGCTTGACACTGAACATTGAGCCTTGAGTGTAGGATAGAGAGGCTTTGAAGTGTGGTACAGTCTGCATGGAGCCGACCTTGAAATACTTTCCTTTATGTTGTTTATGTTCTATACACGTGGTCCCGGTCGTTGCGGACAGTGTACTGGTGGGTAGATTGACTGGGGCGGTCCTCAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGGTCGGACATCAGGAGGTTAGTGCTAATGGCATAAGCCAGCTTGACTGCAGCGTGACGGCGAGGCAGGTGCGAAAGCAGGTCATAGTGATCCGGGGTTCTGAATGCAGGGCCGATCAACGGATAGGTACTCCGGATAACAGGCTGATCCGCCCAAGAGTAAATATAGACGGTGGTGTTTGGCGCGATGTCCGCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATTGTCTTCGCATTTACAATGGTACGCGAGCTGGGTTTAGAACACGGACAAGTTCGGTCCCTTGCGTGGGCGCTGGAGACTGAGGGGGGCTGCTCCTAGTA * AS:i:1583 NM:i:128 MD:Z:14A11^AA0C3A5^C6^TA17G4^T1^CCGAC14^TAAT2^T53C11^GG1^AA2C0G5A9C36^T10^GGT1G18^CGC29C0A0C5^A6G12T1A4^TA0A1^C1^GG25T13^TC4^C1^TAAAG81^G12C1^A31^T10^G1A4^C1^AT2C9^AAA9^GG15^A12T0C4C5C9^CAC1T7^GG1T13G23G1^C1G4^C8^G24^G0T2^T2G1^C11^TA1^C2^C14^A23
U00096.3_3945588_aligned_2 272 gi|556503834|ref|NC_000913.3| 4170526 0 6M1I3M1I2M3I15M2D10M1D6M2D22M1D1M5D14M4D2M1D14M1I26M1I3M1I22M2D1M2D30M1I26M1D10M3D19M1I1M3D37M1D3M1I1M1I9M2I2M1I11M2D2M1D1M2D14M1I25M2D4M1D1M5D33M1I24M1I24M1D14M1D31M1D10M1D6M1D1M2D12M3D9M2D15M1D34M3D9M2D41M1D6M1D6M1I2M1D24M1D3M1D4M1D11M2D1M1D2M1D14M1D23M * 0 0 TCGAAGCCCCGCGAACGTACACGGCGGCCGTGTATTACGGTCTAAGGGCGAAATTCCTTGTCGGCTAAGTCTGCACGAATGGCGGAGGCCAGGCTGTCTCGCACCCGAGACTCAGTGAAATTGAACTGCGCATGTGAAGATGGAGTGTACCCGCCGATAGAAAGGCCCCGTGAAGCTTTACTATACGCTTGACACTGAACATTGAGCCTTGAGTGTAGGATAGAGAGGCTTTGAAGTGTGGTACAGTCTGCATGGAGCCGACCTTGAAATACTTTCCTTTATGTTGTTTATGTTCTATACACGTGGTCCCGGTCGTTGCGGACAGTGTACTGGTGGGTAGATTGACTGGGGCGGTCCTCAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGGTCGGACATCAGGAGGTTAGTGCTAATGGCATAAGCCAGCTTGACTGCAGCGTGACGGCGAGGCAGGTGCGAAAGCAGGTCATAGTGATCCGGGGTTCTGAATGCAGGGCCGATCAACGGATAGGTACTCCGGATAACAGGCTGATCCGCCCAAGAGTAAATATAGACGGTGGTGTTTGGCGCGATGTCCGCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATTGTCTTCGCATTTACAATGGTACGCGAGCTGGGTTTAGAACACGGACAAGTTCGGTCCCTTGCGTGGGCGCTGGAGACTGAGGGGGGCTGCTCCTAGTA * AS:i:1583 NM:i:128 MD:Z:14A11^AA0C3A5^C6^TA17G4^T1^CCGAC14^TAAT2^T53C11^GG1^AA2C0G5A9C36^T10^GGT1G18^CGC29C0A0C5^A6G12T1A4^TA0A1^C1^GG25T13^TC4^C1^TAAAG81^G12C1^A31^T10^G1A4^C1^AT2C9^AAA9^GG15^A12T0C4C5C9^CAC1T7^GG1T13G23G1^C1G4^C8^G24^G0T2^T2G1^C11^TA1^C2^C14^A23
U00096.3_3945588_aligned_2 272 gi|556503834|ref|NC_000913.3| 4211928 0 6M1I3M1I2M3I15M2D10M1D6M2D22M1D1M5D14M4D2M1D14M1I26M1I3M1I22M2D1M2D30M1I26M1D10M3D19M1I1M3D37M1D3M1I1M1I9M2I2M1I11M2D2M1D1M2D14M1I25M2D4M1D1M5D33M1I24M1I24M1D14M1D31M1D10M1D6M1D1M2D12M3D9M2D15M1D34M3D9M2D41M1D6M1D6M1I2M1D24M1D3M1D4M1D11M2D1M1D2M1D14M1D23M * 0 0 TCGAAGCCCCGCGAACGTACACGGCGGCCGTGTATTACGGTCTAAGGGCGAAATTCCTTGTCGGCTAAGTCTGCACGAATGGCGGAGGCCAGGCTGTCTCGCACCCGAGACTCAGTGAAATTGAACTGCGCATGTGAAGATGGAGTGTACCCGCCGATAGAAAGGCCCCGTGAAGCTTTACTATACGCTTGACACTGAACATTGAGCCTTGAGTGTAGGATAGAGAGGCTTTGAAGTGTGGTACAGTCTGCATGGAGCCGACCTTGAAATACTTTCCTTTATGTTGTTTATGTTCTATACACGTGGTCCCGGTCGTTGCGGACAGTGTACTGGTGGGTAGATTGACTGGGGCGGTCCTCAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGGTCGGACATCAGGAGGTTAGTGCTAATGGCATAAGCCAGCTTGACTGCAGCGTGACGGCGAGGCAGGTGCGAAAGCAGGTCATAGTGATCCGGGGTTCTGAATGCAGGGCCGATCAACGGATAGGTACTCCGGATAACAGGCTGATCCGCCCAAGAGTAAATATAGACGGTGGTGTTTGGCGCGATGTCCGCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATTGTCTTCGCATTTACAATGGTACGCGAGCTGGGTTTAGAACACGGACAAGTTCGGTCCCTTGCGTGGGCGCTGGAGACTGAGGGGGGCTGCTCCTAGTA * AS:i:1583 NM:i:128 MD:Z:14A11^AA0C3A5^C6^TA17G4^T1^CCGAC14^TAAT2^T53C11^GG1^AA2C0G5A9C36^T10^GGT1G18^CGC29C0A0C5^A6G12T1A4^TA0A1^C1^GG25T13^TC4^C1^TAAAG81^G12C1^A31^T10^G1A4^C1^AT2C9^AAA9^GG15^A12T0C4C5C9^CAC1T7^GG1T13G23G1^C1G4^C8^G24^G0T2^T2G1^C11^TA1^C2^C14^A23
U00096.3_3945588_aligned_2 256 gi|556503834|ref|NC_000913.3| 3424127 0 22M1D14M1D2M2D1M1D12M1D4M1D2M1D25M1D2M1I5M1D7M1D1M1I2M1D34M2D9M3D37M1D13M2D10M3D12M3D5M1D13M1D31M1D14M1D24M1I22M1I33M2D1M2D1M2D2M1D1M1D27M1I13M2D1M1D2M2D10M2I2M1I8M1I2M1I4M1D37M3D2M1I16M2D1M1D12M1D26M1I25M1D1M1D1M1D2M1D24M1I3M1I26M1I14M1D2M4D13M5D1M1D23M2D5M1D10M2D12M1I1M3I3M1I11M * 0 0 TACTAGGAGCAGCCCCCCTCAGTCTCCAGCGCCCACGCAAGGGACCGAACTTGTCCGTGTTCTAAACCCAGCTCGCGTACCATTGTAAATGCGAAGACAATACCCTTGGGACCTACTTCAGCTCCAGGATGTGATGCGGACATCGCGCCAAACACCACCGTCTATATTTACTCTTGGGCGGATCAGCCTGTTATCCGGAGTACCTATCCGTTGATCGGCCCTGCATTCAGAACCCCGGATCACTATGACCTGCTTTCGCACCTGCCTCGCCGTCACGCTGCAGTCAAGCTGGCTTATGCCATTAGCACTAACCTCCTGATGTCCGACCCAGGATTAGCCAACCTTCGTGCTCCTCCGTTACTGAGGACCGCCCCAGTCAATCTACCCACCAGTACACTGTCCGCAACGACCGGGACCACGTGTATAGAACATAAACAACATAAAGGAAAGTATTTCAAGGTCGGCTCCATGCAGACTGTACCACACTTCAAAGCCTCTCTATCCTACACTCAAGGCTCAATGTTCAGTGTCAAGCGTATAGTAAAGCTTCACGGGGCCTTTCTATCGGCGGGTACACTCCATCTTCACATGCGCAGTTCAATTTCACTGAGTCTCGGGTGCGAGACAGCCTGGCCTCCGCCATTCGTGCAGACTTAGCCGACAAGGAATTTCGCCCTTAGACCGTAATACACGGCCGCCGTGTACGTTCGCGGGGCTTCGA * AS:i:1574 NM:i:130 MD:Z:22^T14^G2^AG1^T12^G1C2^A2^A0C24^C7^G5C1^G3^C21C12^GA2C6^GAG1T10G5G4G0A12^T13^CC10^TTT10G1^GAT5^T1C11^A31^T1G12^C79^CT1^TT1^AG2^G1^A15A24^CC1^G2^TT0A4T1A12C5^T6G0T0G28^GGC11T6^CC1^A0C11^A36G9T4^C1^G1^C0T1^G1C11G53^A2^ATTA13^GGTCG1^A5C17^TA5^G6T3^GT0T13A12
U00096.3_3945588_aligned_2 272 gi|556503834|ref|NC_000913.3| 227644 0 6M1I3M1I2M3I15M2D10M1D6M2D22M1D1M5D14M4D2M1D14M1I26M1I3M1I22M2D1M2D30M1I26M1D10M3D19M1I1M3D37M1D3M1I1M1I9M2I2M1I11M2D2M1D1M2D14M1I25M2D4M1D1M5D33M1I24M1I24M1D14M1D31M1D10M1D6M1D1M2D12M3D9M2D15M1D34M3D9M2D41M1D6M1D6M1I2M1D24M1D3M1D4M1D11M2D1M1D2M1D14M1D23M * 0 0 TCGAAGCCCCGCGAACGTACACGGCGGCCGTGTATTACGGTCTAAGGGCGAAATTCCTTGTCGGCTAAGTCTGCACGAATGGCGGAGGCCAGGCTGTCTCGCACCCGAGACTCAGTGAAATTGAACTGCGCATGTGAAGATGGAGTGTACCCGCCGATAGAAAGGCCCCGTGAAGCTTTACTATACGCTTGACACTGAACATTGAGCCTTGAGTGTAGGATAGAGAGGCTTTGAAGTGTGGTACAGTCTGCATGGAGCCGACCTTGAAATACTTTCCTTTATGTTGTTTATGTTCTATACACGTGGTCCCGGTCGTTGCGGACAGTGTACTGGTGGGTAGATTGACTGGGGCGGTCCTCAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGGTCGGACATCAGGAGGTTAGTGCTAATGGCATAAGCCAGCTTGACTGCAGCGTGACGGCGAGGCAGGTGCGAAAGCAGGTCATAGTGATCCGGGGTTCTGAATGCAGGGCCGATCAACGGATAGGTACTCCGGATAACAGGCTGATCCGCCCAAGAGTAAATATAGACGGTGGTGTTTGGCGCGATGTCCGCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATTGTCTTCGCATTTACAATGGTACGCGAGCTGGGTTTAGAACACGGACAAGTTCGGTCCCTTGCGTGGGCGCTGGAGACTGAGGGGGGCTGCTCCTAGTA * AS:i:1583 NM:i:128 MD:Z:14A11^AA0C3A5^C6^TA17G4^T1^CCGAC14^TAAT2^T53C11^GG1^AA2C0G5A9C36^T10^GGT1G18^CGC29C0A0C5^A6G12T1A4^TA0A1^C1^GG25T13^TC4^C1^TAAAG81^G12C1^A31^T10^G1A4^C1^AT2C9^AAA9^GG15^A12T0C4C5C9^CAC1T7^GG1T13G23G1^C1G4^C8^G24^G0T2^T2G1^C11^TA1^C2^C14^A23Thanks,
Hajime Suzuki
npavlovikj
commented
6 years ago Dear @ocxtal , thank you so much for fixing this issue in a timely manner! I re-ran my sequences that failed earlier, and everything aligned successfully this time. Thanks again! Natasha
Hello,
I am trying to align some Pacbio reads using this command, after having built the index:
minialign -l ref_index.mai SubPacbio.fq > out.samThis returns
Any idea of what's happening?