Compare two or more BAM files

This program is now part of the main `jvarkit`

tool. See jvarkit for compiling.

```
Usage: java -jar dist/jvarkit.jar cmpbams [options] Files
Usage: cmpbams [options] Files
Options:
-c, --cigar
use cigar String for comparaison
Default: false
-d, --distance
distance tolerance between two alignments
Default: 10
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-Q, --mapq
min MAPQ
Default: 0
--maxRecordsInRam
When writing files that need to be sorted, this will specify the number
of records stored in RAM before spilling to disk. Increasing this number
reduces the number of file handles needed to sort a file, and increases
the amount of RAM needed
Default: 50000
--no-filter
Do not filter the reads. Default is to ignore secondary or supplementary
alignments.
Default: false
-o, --output
Output file. Optional . Default: stdout
-R, --reference
For CRAM. Indexed fasta Reference file. This file must be indexed with
samtools faidx and with picard/gatk CreateSequenceDictionary or samtools
dict
-r, --region
An interval as the following syntax : "chrom:start-end" or
"chrom:middle+extend" or "chrom:start-end+extend" or
"chrom:start-end+extend-percent%".A program might use a Reference
sequence to fix the chromosome name (e.g: 1->chr1)
Default: <empty string>
-F, --sam
use sam flag for comparaison
Default: false
--tmpDir
tmp working directory. Default: java.io.tmpDir
Default: []
--version
print version and exit
```

- sam
- bam
- compare

20130506

- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit

The project is licensed under the MIT license.

Should you cite **cmpbams** ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Question was : “mapping with BWA produced a variation one year ago. We then mapped the same fastq with two different sets of parameters, but we cannot find the variant anymore. Has the mapping changed ?”

Extract the read names from the original BAM:

```
samtools view file1.bam K01:2179-2179 |\
cut -d ' ' -f 1 | sort | uniq > names.txt
```

Use [[SamGrep]] to retieve the reads in the 3 bams:

```
java -jar dist/samgrep.jar -f names.txt file1.bam > tmp1.sam
java -jar dist/samgrep.jar -f names.txt file2.bam > tmp2.sam
java -jar dist/samgrep.jar -f names.txt file3.bam > tmp3.sam
```

Run CmpBams

```
$ java -jar dist/cmpbams.jar -F -C tmp1.sam tmp2.sam tmp3.sam
#READ-Name tmp1.sam tmp2.sam|tmp1.sam tmp3.sam|tmp2.sam tmp3.sam tmp1.sam tmp2.sam tmp3.sam
HWI-1KL149:20:C1CU7ACXX:1:1101:17626:32431/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:1101:17626:32431/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1102:16831:71728/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1102:16831:71728/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1105:3309:27760/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1105:3309:27760/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1106:2914:12111/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:1106:2914:12111/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1107:11589:17295/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:1107:11589:17295/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1110:14096:95943/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:1110:14096:95943/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1110:15369:59046/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1110:15369:59046/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1111:8599:97362/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1111:8599:97362/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1113:10490:30873/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1113:10490:30873/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1113:12360:36316/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1113:12360:36316/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1113:4589:62685/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:1113:4589:62685/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1115:7288:99676/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1115:7288:99676/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1116:8136:52921/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1116:8136:52921/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1202:11809:66877/1 EQ|EQ|EQ K01:2104=83/100M K01:2104=83/100M K01:2104=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1202:11809:66877/2 EQ|EQ|EQ K01:2043=163/100M K01:2043=163/100M K01:2043=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1202:18844:98575/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1202:18844:98575/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1205:20782:28689/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1205:20782:28689/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1206:10108:83718/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:1206:10108:83718/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1212:17964:23344/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:1212:17964:23344/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1213:9111:56546/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1213:9111:56546/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1216:4380:98965/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1216:4380:98965/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1216:4493:85995/1 EQ|NE|NE K01:2143=83/36S36M3I25M K01:2143=83/36S36M3I25M K01:2107=83/72M3I25M
HWI-1KL149:20:C1CU7ACXX:1:1216:4493:85995/2 EQ|EQ|EQ K01:2043=163/100M K01:2043=163/100M K01:2043=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1216:8034:78319/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1216:8034:78319/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1316:14751:4679/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:1316:14751:4679/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2102:4725:60173/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:2102:4725:60173/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2104:19271:24502/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:2104:19271:24502/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2104:2016:81735/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2104:2016:81735/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2110:4445:72697/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:2110:4445:72697/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2111:2256:47748/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:2111:2256:47748/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2115:12497:79931/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:2115:12497:79931/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2115:17576:9737/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:2115:17576:9737/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2116:7977:30610/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2116:7977:30610/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2201:16984:100451/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2201:16984:100451/2 EQ|EQ|EQ K01:2059=163/87M13S K01:2059=163/87M13S K01:2059=163/87M13S
HWI-1KL149:20:C1CU7ACXX:1:2203:19912:68616/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2203:19912:68616/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2204:13318:18341/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2204:13318:18341/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2206:10726:12303/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2206:10726:12303/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2206:11557:78671/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2206:11557:78671/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2211:12806:63973/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2211:12806:63973/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2212:17602:62052/1 EQ|EQ|EQ K01:2104=83/100M K01:2104=83/100M K01:2104=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2212:17602:62052/2 EQ|EQ|EQ K01:2043=163/100M K01:2043=163/100M K01:2043=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2212:19408:52552/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2212:19408:52552/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2303:8733:45438/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2303:8733:45438/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2304:9806:12935/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2304:9806:12935/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2305:12165:42334/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:2305:12165:42334/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2305:2388:67842/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2305:2388:67842/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2307:14199:91258/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2307:14199:91258/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2307:3121:93985/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2307:3121:93985/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2309:13907:13532/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2309:13907:13532/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2309:20396:57002/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:2309:20396:57002/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2312:11602:6630/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2312:11602:6630/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2313:11868:31327/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2313:11868:31327/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2313:9555:94108/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:2313:9555:94108/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2315:19820:15046/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2315:19820:15046/2 EQ|EQ|EQ K01:2081=163/99M1S K01:2081=163/99M1S K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1101:18362:28315/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1101:18362:28315/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1105:18846:45527/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1105:18846:45527/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1105:5659:65125/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1105:5659:65125/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1108:9609:39170/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1108:9609:39170/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1110:2262:8369/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1110:2262:8369/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1111:18496:5547/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1111:18496:5547/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1112:10132:23322/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1112:10132:23322/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1112:7260:56414/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1112:7260:56414/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1201:6906:82750/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:2:1201:6906:82750/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1202:16231:100362/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1202:16231:100362/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1213:12574:89489/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:2:1213:12574:89489/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1214:20898:3105/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1214:20898:3105/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:```20:C1CU7ACXX:2:1214:7035:46585/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1214:7035:46585/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1215:19107:31048/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1215:19107:31048/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1216:15500:73171/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:2:1216:15500:73171/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1216:6409:43952/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1216:6409:43952/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1301:16595:88662/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1301:16595:88662/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1306:12619:24138/1 EQ|NE|NE K01:2143=83/36S36M3I25M K01:2143=83/36S36M3I25M K01:2107=83/72M3I25M
HWI-1KL149:20:C1CU7ACXX:2:1306:12619:24138/2 EQ|EQ|EQ K01:2043=163/100M K01:2043=163/100M K01:2043=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1308:8618:21991/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:2:1308:8618:21991/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1309:15540:69632/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1309:15540:69632/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1314:9489:93274/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1314:9489:93274/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1316:5692:99314/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1316:5692:99314/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2108:14003:59876/1 EQ|EQ|EQ K01:2136=83/44M3I53M K01:2136=83/44M3I53M K01:2136=83/44M3I53M
HWI-1KL149:20:C1CU7ACXX:2:2108:14003:59876/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2113:14713:81195/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2113:14713:81195/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2114:13002:89288/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2114:13002:89288/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2201:11170:94334/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:2:2201:11170:94334/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2202:4380:42920/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2202:4380:42920/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2213:14141:87844/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2213:14141:87844/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2213:15510:90052/1 EQ|EQ|EQ K01:2122=83/57M3I23M1D17M K01:2122=83/57M3I23M1D17M K01:2122=83/57M3I23M1D17M
HWI-1KL149:20:C1CU7ACXX:2:2213:15510:90052/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2213:1759:92031/1 EQ|EQ|EQ K01:2123=83/56M3I41M K01:2123=83/56M3I41M K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:2:2213:1759:92031/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:14279:12564/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:14279:12564/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:16028:26845/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:16028:26845/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:16774:44335/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:16774:44335/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2301:16926:82641/1 EQ|EQ|EQ K01:2136=83/43M3I54M K01:2136=83/43M3I54M K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:2:2301:16926:82641/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2309:5711:82879/1 EQ|EQ|EQ K01:2120=83/100M K01:2120=83/100M K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2309:5711:82879/2 EQ|EQ|EQ K01:1990=163/100M K01:1990=163/100M K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2310:13450:61828/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2310:13450:61828/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2311:14082:99026/1 EQ|EQ|EQ K01:2213=83/100M K01:2213=83/100M K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2311:14082:99026/2 EQ|EQ|EQ K01:2081=163/100M K01:2081=163/100M K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2315:4940:7934/1 EQ|EQ|EQ K01:2133=83/100M K01:2133=83/100M K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2315:4940:7934/2 EQ|EQ|EQ K01:2059=163/100M K01:2059=163/100M K01:2059=163/100M</h:pre>
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- Alejandra Bodelon, Marie Fablet, Philippe Veber, Cristina Vieira, Maria Pilar Garcia Guerreiro, High stability of the epigenome in Drosophila interspecific hybrids, Genome Biology and Evolution, 2022;, evac024, https://doi.org/10.1093/gbe/evac024
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