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OpenGene / MutScan

Detect and visualize target mutations by scanning FastQ files directly
MIT License
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MutScan didn't find any mutation #8

Closed zlangley closed 5 years ago

zlangley commented 5 years ago

After compiling MutScan from source, I have not been able to run it successfully on the test data provided in the repository. I ran the command in the README, which gave the following output:

testdata$ mutscan -1 R1.fq.gz -2 R2.fq.gz
MutScan didn't find any mutation

mutscan -1 R1.fq.gz -2 R2.fq.gz
Mutscan v1.14.0, time used: 1 seconds

Am I doing something wrong?

sfchen commented 5 years ago

time used: 1 seconds

Seems that your files are very small?

Please check the downloaded files by comparing the MD5

sfchen commented 5 years ago

Here is my output

MacBook-Pro:MutScan shifu$ ./mutscan -1 R1.fq.gz -2 R2.fq.gz

---------------
NRAS-neg-1-115258748-2-c.34G>T-p.G12C-COSM562 GGATTGTCAGTGCGCTTTTCCCAACACCAC A TGCTCCAACCACCACCAGTTTGTACTCAGT chr1
1, pos: 166, distance: 0, reverse
@NB551106:59:HTFV3BGX2:1:11102:9413:4074 1:N:0:AGTCAA merged offset:78 overlap:71 diff:0
CCTCTTATTCCTTTAATACAGAATATGGGTAAAGATGATCCGACAAGTGAGAGACAGGATCAGGTCAGCGGGCTACCACTGGGCCTCACCTCTATGGTGGGATCATATTCATCTACAAAGTGGTTCTGGATTAGCT GGATTGTCAGTGCGCTTTTCCCAACACCAC A TGCTCCAACCACCACCAGTTTGTACTCAGT CATTTCACACCAGCAAGAACCTGTTGGAAACC
-
AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEeeiiieieiiiiiiieeieeeiiiiiiSiiieiiiieiiiiiiieiieeiiiiiii eiieiiiiiiiii``EEEEAEEEEEEEEEE E AEEEEEEEEEEEEEEEEE/EEEEEEEEEEE EEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA
2, pos: 80, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:13201:15696:12851 1:N:0:GATCAG merged offset:0 overlap:145 diff:0
CACCTCTATGGTGGGATCATATTCATCTACAAAGTGGTTCTGGATTAGCT GGATTGTCAGTGCGCTTTTCCCAACACCAC A TGCTCCAACCACCACCAGTTTGTACTCAGT CATTTCACACCAGCAAGAACCTGTTGGAAACCAG
-
eeeeeiieie`ieS`iieeiiiiiieeiiiiiiiiiiS`iiiiiiiiiii i`iiei`iiiiiiiiiiiiiiiiiiiiiii S iiiiiiieiiSiiiiiiiiiiiiiiiiiii ieiiieei`e`i`iiSSS`e`eSZeiiiieaaee

---------------
EGFR-pos-7-55249071-20-c.2369C>T-p.T790M-COSM6240 TCTGCCTCACCTCCACCGTGCAGCTCATCA T GCAGCTCATGCCCTTCGGCTGCCTCCTGGA chr7
1, pos: 132, distance: 1, forward
@NB551106:9:H5Y5GBGX2:1:21107:14365:13681 1:N:0:GATCAG
CTGGCCACCATGCGAAGCCACACTGACGTGCCTCTCCCTCCCTCCAGGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTGCCGCCTGCTGGGCA TCTGCCTCACCTCCACCGTGCAGCTCATCA T GCAGCTCAGGCCCTTCGG 
+
AAAAAEEEAAEEEAEEAEEEEEEEE/AEEEEEEEEEEEEEEEEEE<A<AAEEEEEEEEAEA<<EEEEEAEEE/E/AEEAEE/EEA/EEEAEEAA<AAEEEEA /EEEEE<E/EA<EA/E/EA/EE/<AEA<EE < A6/E<6<E/A/EAE/<</ 
2, pos: 102, distance: 1, reverse
@NB551106:9:H5Y5GBGX2:1:21107:14365:13681 2:N:0:GATCAG
CCTCTCCCTCCCTCCCGGATGCCTACGTGATGGCCAGCGTGGACATCCCCCACGTGTGCCGCCTGCTGGGCA TCTGCCTCACCTCCACCGTGCAGCTCATCA T GCAGCTCATGCCCTTCGGCTCCCTCCTGGA CTATGTCCGGGAACACAA
-
<</EEAA///AEA/</A<</E6<<//E/E6/AEE</<AE/EE/A//AEE/6/<E/EAEAAEEAEEA6EAAEE EEAEA/EEEAAEEA/AAEAEAAEE/E/EEE E AEA/EEEAEAEEAEEEEEEEEAEEEEEEEE EEEEEE/EEEEEE6A/AA
3, pos: 97, distance: 2, forward
@NB551106:9:H5Y5GBGX2:1:13107:23878:9922 1:N:0:GATCAG merged offset:0 overlap:121 diff:0
CCCTCCCTCCAGGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTGCCGCCTGCTGGGCA TCTGCCTCACCTCCACCGTGCAGCTCATCA T GCAGCTCATGCCCTTCGGAAGCC 
+
eeeaeiieieeS`SeeiieSi`ii`iiiiiiiiiSeiaieeiiiiieiieieiiiiiiiiieiiiii iiiieiai`ieiiiSiiieiiSiiiiSei` e iSeiiiiSiiiiie`iiiOOeeO 
4, pos: 78, distance: 1, forward
@NB551106:9:H5Y5GBGX2:1:12302:13931:19052 1:N:0:GATCAG merged offset:29 overlap:122 diff:0
ACGTGATGGCCAGCGTGGACAACCCCCACGTGTGCCGCCTGCTGGGCA TCTGCCTCACCTCCACCGTGCAACTCATCA T GCAGCTCATGCCCTTCGGCTGCCTCCTGGA CTATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGG
+
AAAAAEEEEEEEEEEEEEEEEEEEEEEEEeSSiie`e`eii`SieeeO `eee`iiiOieii`Viii`SeOSiieiiee ` ie`iiiieiiiiiieiiiiiiiiiiii`iS SZSiieiiiiiSeiSiieieiSSi`e`eii`ZS``ei`eeiSEEEEEEEEEEEEEEEEEEEEEEEEAAAAA
5, pos: 60, distance: 2, reverse
@NB551106:9:H5Y5GBGX2:1:21312:26680:10752 1:N:0:GATCAG
CGCAGCTCCCCGTGTGCCGCCTGCTGGGCA TCTGCCTCACCTCCAGCGTGCAGCTCATCA T GCAGCTCATGCCCTTCGGCTCCCTCCTGGA CTATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCA
-
///////<///A/E/E//E/AEE<AAA//< /A/EEEE///A</E///A</E/AE/EAE// E /66EE/EAEE/EEEAAEEEEEEEE/AEEE/ EEEEEEAE/AEEAE/EEE/E/E/EEAEEEE6EEE//EAE/EEAEEEAEEEAEEAEA6AAA
6, pos: 51, distance: 1, forward
@NB551106:9:H5Y5GBGX2:1:13201:25711:16931 2:N:0:GATCAG
ACGTGTGCCGCCTGCTGGGCA TCTGCCTCACCTCCACCGTGCAGCTCATCA T GCAGCTCATGCCCTTCGGCTCCCTCCTGGA CTATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAA
+
AAAAAEEEEEEEEEEEEEEEE EEEEEEEEEEEEEEEEAAEEEEEAEEEEEE E EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE EEEEEEEEEEAEEEAEEEAE/EEEAEEEEEEEEA/<EEEAEAEAEEEE<AA<A/AAEEAE//A<<EEE
7, pos: 48, distance: 1, reverse
@NB551106:9:H5Y5GBGX2:1:21310:7418:7755 1:N:0:GATCAG merged offset:0 overlap:125 diff:0
TGTGCCGCCTGCTGGGCA TCTGCCTCACCTCCACCGTGCAGCTCATCA T GCAGCTCATGCCCTTCGGCTCCCTCCTGGA CTATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTC
-
aeOeeiieiiiiiieiii ieiiiiiiSiiiiiZiiiiiiiiiSiiiii i iieiiiiZiiiiiiiiiiieiiiiiiiiSe iiieSiSi`eiSeeSeiiiiSeZi``iiiiieiSeiiSOSie\eOe
8, pos: 48, distance: 2, reverse
@NB551106:9:H5Y5GBGX2:1:13201:25711:16931 1:N:0:GATCAG
GGTGCCGCCTGCTGGGCA TCTGCCTCACCTCCCCCGTGCAGCTCATCA T GCAGCTCATGCCCTTCGGCTCCCTCCTGGA CTATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGT
-
<//6E<AEE<A<E<A<A< E/E<A</E/EAEEE/EEEEAE/EEEAEEEA E EA/EE/EEEEEEEE/EEEEEEEEEEE/EEE EEEEEEEEAEEEEEEEEEEEEE6EE/EEEEEEEEEEEEEEEEEE6EEEEEEEEE/E/EEEEEEEEEEAAAA/
9, pos: 26, distance: 2, reverse
@NB551106:9:H5Y5GBGX2:1:11207:19779:6631 1:N:0:GATCAG merged offset:0 overlap:149 diff:1
 CCTCACCTCCACCGTGCAGCTCATCA T GCAGCTCATGCCCTTCGGAAGCCTCCTGGA CTATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGTAATCAGGGAAGGGAGATACG
-
 eeQa\ieiiOiaSVSZiiii`iOiii i iiiii`S`Siiiiiie`ie`iie`iSiiSe iiiieSiiieiSSSSiiiieZiiieiiSSiiiieieSeeiSeiieiiAiieiJiSiieieiSSeeO\SiiSiei`iie`SSeSeieiVVOOa
10, pos: 26, distance: 2, reverse
@NB551106:9:H5Y5GBGX2:1:11307:24343:19438 1:N:0:GATCAG merged offset:0 overlap:149 diff:0
 CCTCACCTCCACCGTGCAGCTCATCA T GCAGCTCATGCCCTTCGGAAGCCTCCTGGA CTATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGTAATCAGGGAAGGGAGATACG
-
 \aa\VeiSe`\eiS`iieiiei`eeS i SiZSeieeiieSiS`iiiaSiiiiiiiSii iieiieiieiie`i`ieiiiSiiiiiiiiiiSiiieiiaeiiiiii`eiiiii`OiiiiiiSeiiiiiiiiiSeS`iie`iee`e`eOOaea
11, pos: 19, distance: 2, reverse
@NB551106:9:H5Y5GBGX2:1:11101:3081:15503 1:N:0:GATCAG merged offset:0 overlap:144 diff:2
 TCCACCGTGCAGCTCATCA T GCAGCTCATGCCCTTCGGAAGCCTCCTGGA CTATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGTAATCAGGGAAGGGAGATACGGG
-
 OeAeaSi`eeVeSieiiii ` SeieSiei`iOJiiieeieiSiiiSiiiie iiiSiSieeSiSiiiiiiii`ieeiiiieeieZiZZiiiiiiee\ZeiiiaiiiS``eiiiE`S`Sai`eieiS`eeieeiieSZeeieOVO\V

---------------
EGFR-pos-7-55249091-20-c.2389T>A-p.C797S-COSM5010368 CAGCTCATCACGCAGCTCATGCCCTTCGGC A GCCTCCTGGACTATGTCCGGGAACACAAAG chr7
1, pos: 46, distance: 2, reverse
@NB551106:9:H5Y5GBGX2:1:11207:19779:6631 1:N:0:GATCAG merged offset:0 overlap:149 diff:1
CCTCACCTCCACCGTG CAGCTCATCATGCAGCTCATGCCCTTCGGA A GCCTCCTGGACTATGTCCGGGAACACAAAG ACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGTAATCAGGGAAGGGAGATACG
-
eeQa\ieiiOiaSVSZ iiii`iOiiiiiiiii`S`Siiiiiie`ie ` iie`iSiiSeiiiieSiiieiSSSSiiiie ZiiieiiSSiiiieieSeeiSeiieiiAiieiJiSiieieiSSeeO\SiiSiei`iie`SSeSeieiVVOOa
2, pos: 46, distance: 2, reverse
@NB551106:9:H5Y5GBGX2:1:11307:24343:19438 1:N:0:GATCAG merged offset:0 overlap:149 diff:0
CCTCACCTCCACCGTG CAGCTCATCATGCAGCTCATGCCCTTCGGA A GCCTCCTGGACTATGTCCGGGAACACAAAG ACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGTAATCAGGGAAGGGAGATACG
-
\aa\VeiSe`\eiS`i ieiiei`eeSiSiZSeieeiieSiS`iiia S iiiiiiiSiiiieiieiieiie`i`ieiii SiiiiiiiiiiSiiieiiaeiiiiii`eiiiii`OiiiiiiSeiiiiiiiiiSeS`iie`iee`e`eOOaea
3, pos: 39, distance: 2, reverse
@NB551106:9:H5Y5GBGX2:1:11101:3081:15503 1:N:0:GATCAG merged offset:0 overlap:144 diff:2
TCCACCGTG CAGCTCATCATGCAGCTCATGCCCTTCGGA A GCCTCCTGGACTATGTCCGGGAACACAAAG ACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGTAATCAGGGAAGGGAGATACGGG
-
OeAeaSi`e eVeSieiiii`SeieSiei`iOJiiieeie i SiiiSiiiieiiiSiSieeSiSiiiiiiii `ieeiiiieeieZiZZiiiiiiee\ZeiiiaiiiS``eiiiE`S`Sai`eieiS`eeieeiieSZeeieOVO\V
4, pos: 28, distance: 2, forward
@NB551106:9:H5Y5GBGX2:1:11210:13966:15731 2:N:0:GATCAG
 GCTCATCATGCAGCTCATGCCCTTCGGA A GCCTCCTGGACTATGTCCGGGAACACAAAG ACAATATTGGCTCCCAGTACCTGCTCAACCGGTGTGTGCAGATCGCAAAGGTAATCAGGGAAGGGAGATACGGGGAGGGGAGAGTCGGAGCC
+
 AAAAAEEEAEEAEEEEEEEEEEAEEEEE A EEEEEEEEEAEEEEEEEEEEEE/E6EEEEE //EAAEEEEEEEEEE<AE/EEEEAEE//EEE6A<EEEE/EE/<EEE/EEAE<E//EE<EE//6<<AE/E/<AA<A/EAA6A/A///6</6</

---------------
EGFR-pos-7-55249092-20-c.2390G>C-p.C797S-COSM5010368 AGCTCATCACGCAGCTCATGCCCTTCGGCT C CCTCCTGGACTATGTCCGGGAACACAAAGA chr7
1, pos: 123, distance: 1, reverse
@NB551106:9:H5Y5GBGX2:1:21107:14365:13681 2:N:0:GATCAG
CCTCTCCCTCCCTCCCGGATGCCTACGTGATGGCCAGCGTGGACATCCCCCACGTGTGCCGCCTGCTGGGCATCTGCCTCACCTCCACCGTGC AGCTCATCATGCAGCTCATGCCCTTCGGCT C CCTCCTGGACTATGTCCGGGAACACAA 
-
<</EEAA///AEA/</A<</E6<<//E/E6/AEE</<AE/EE/A//AEE/6/<E/EAEAAEEAEEA6EAAEEEEAEA/EEEAAEEA/AAEAEA AEE/E/EEEEAEA/EEEAEAEEAEEEEEEE E AEEEEEEEEEEEEEE/EEEEEE6A/AA 
2, pos: 81, distance: 1, reverse
@NB551106:9:H5Y5GBGX2:1:21312:26680:10752 1:N:0:GATCAG
CGCAGCTCCCCGTGTGCCGCCTGCTGGGCATCTGCCTCACCTCCAGCGTGC AGCTCATCATGCAGCTCATGCCCTTCGGCT C CCTCCTGGACTATGTCCGGGAACACAAAGA CAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCA
-
///////<///A/E/E//E/AEE<AAA//</A/EEEE///A</E///A</E /AE/EAE//E/66EE/EAEE/EEEAAEEEE E EEE/AEEE/EEEEEEAE/AEEAE/EEE/E/ E/EEAEEEE6EEE//EAE/EEAEEEAEEEAEEAEA6AAA
3, pos: 72, distance: 1, forward
@NB551106:9:H5Y5GBGX2:1:13201:25711:16931 2:N:0:GATCAG
ACGTGTGCCGCCTGCTGGGCATCTGCCTCACCTCCACCGTGC AGCTCATCATGCAGCTCATGCCCTTCGGCT C CCTCCTGGACTATGTCCGGGAACACAAAGA CAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAA
+
AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEE EEAEEEEEEEEEEEEEEEEEEEEEEEEEEE E EEEEEEEEEEEEEEEEEEEAEEEAEEEAE/ EEEAEEEEEEEEA/<EEEAEAEAEEEE<AA<A/AAEEAE//A<<EEE
4, pos: 69, distance: 1, reverse
@NB551106:9:H5Y5GBGX2:1:21310:7418:7755 1:N:0:GATCAG merged offset:0 overlap:125 diff:0
TGTGCCGCCTGCTGGGCATCTGCCTCACCTCCACCGTGC AGCTCATCATGCAGCTCATGCCCTTCGGCT C CCTCCTGGACTATGTCCGGGAACACAAAGA CAATATTGGCTCCCAGTACCTGCTC
-
aeOeeiieiiiiiieiiiieiiiiiiSiiiiiZiiiiii iiiSiiiiiiiieiiiiZiiiiiiiiiiie i iiiiiiiSeiiieSiSi`eiSeeSeiiiiS eZi``iiiiieiSeiiSOSie\eOe
5, pos: 69, distance: 1, reverse
@NB551106:9:H5Y5GBGX2:1:13201:25711:16931 1:N:0:GATCAG
GGTGCCGCCTGCTGGGCATCTGCCTCACCTCCCCCGTGC AGCTCATCATGCAGCTCATGCCCTTCGGCT C CCTCCTGGACTATGTCCGGGAACACAAAGA CAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGT
-
<//6E<AEE<A<E<A<A<E/E<A</E/EAEEE/EEEEAE /EEEAEEEAEEA/EE/EEEEEEEE/EEEEE E EEEEE/EEEEEEEEEEEAEEEEEEEEEEEE E6EE/EEEEEEEEEEEEEEEEEE6EEEEEEEEE/E/EEEEEEEEEEAAAA/
6, pos: 17, distance: 1, forward
@NB551106:9:H5Y5GBGX2:1:12311:3352:1406 2:N:0:GATCAG
 GCTCATGCCCTTCGGCT C CCTCCTGGACTATGTCCAGGAACACAAAGA CAAAATAGGCTCCCAGAACCAGCTCAACTGGTGTGTGCAGCACGCAAACGTAATCAGGGAAGGCAGCTACGGGGAGGGGAGATAAGTCGCCAGGCGCCGCACC
+
 AAAA/A/EEE/AEEEEE 6 EE/EE/EE/EEEA//EAE/E//E//AE/// EEE/E///6EE6EE///<EE/E/E/E/A<////EE/<6E///E/E<<E/E/<A/E<////A/EA/E///<A/EA///A///////////<//////A</EEA/

---------------
EGFR-pos-7-55242465:55242479-c.2235_2249del15-p.E746_A750delELREA-COSM6223 TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT chr7
1, pos: 170, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:22307:15360:1044 1:N:0:GATCAG merged offset:94 overlap:57 diff:0
CACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCA
+
AAAAAEEEEEEEEEEEEEEAEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEE/EEAEEEEEEEEEEEAEEEA/E<EEEEAEEE/EEEEEEEAS`\`aO``SeeeS`J`\`SaeeaWJe=\ei`ieeieS```Z`ieiiie OeieeSeeSEEEEAEEEEEEEAEEEEEE EEAE AAEEEEEEEAEEEEEEEEEEEEEEEEEE EEEEEEEEEAEEEEEEEEEEEEEEEAEEEEEEEEEEEAAAAA
2, pos: 140, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:11309:4551:3202 1:N:0:GATCAG merged offset:63 overlap:87 diff:0
GCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCT
-
AAAAAEEEEEEEEEEEEEAEEEEEAEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEe`eZZSe`Seei`iiiieeeiei`eeea`iiieeiieii``iiiiiie ieSiiiiiiiiiiiiiiei`We`i`e`e iie` iiiieeZEEEEEEEEEEEEEEEEEEEEE EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA
3, pos: 125, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:21303:20073:9645 1:N:0:GATCAG merged offset:50 overlap:100 diff:0
TCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTG
-
AAAAAEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEZ`iSaeii`iie`eeiiiSeOSeeiSiiieiieeiiJiiiiiiiSee eiee`eiiSiieii`iii`Siiii`Sii iiii ieieaZeeeii`iiiiiiieiEEEEEEE EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEAAAAA
4, pos: 123, distance: 2, forward
@NB551106:9:H5Y5GBGX2:1:21107:2005:9896 1:N:0:GATCAG
CACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCATCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTACGAAAGCCCACAAGGAA 
+
A6AAAEAEEA/EEEE//AEEEE6EEE//E/EEAE/EEAE/AAE<//E/EEEE<E6E///<EEEAEEE//AA//EEAAEEEEE/A/E<A<EEEEEE //AEAEEEE//E</E/</E/EE/A//<A EEAE EA/A<//6AE/A6A/<<E/<//< 
5, pos: 123, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:22310:18260:8674 1:N:0:GATCAG merged offset:40 overlap:110 diff:0
CACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCA
+
AAAAAEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEiiiiiiie`eieSiiiiiiieieiiiiiiieii`iiiiiiiiiieiiiiiiiiei iiiiiiiiii`iiieii``e\iieeeii iieS iie`eSeJiiiiieieiiiii`iEEEEE EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA
6, pos: 123, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:21306:3386:1754 1:N:0:GATCAG merged offset:40 overlap:111 diff:1
CACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCA
+
A/AAAEEAEAEEEEEEEAEEEEEEEEE6EE/EEEEEEE/E`\`OS`ZeZQa\SSeiiiiiiiiiiiei`SeeiiaSiii`iiie`O`iiiiS\ei eieiiSQSSiiieSii`ii`SSaae`Oa e`aJ S`ieiiiWiiSSei`eii`SiSZEEEEE EEEEEEEEEEEEEEEEEEEEAAEEEAEEEEAAAAA
7, pos: 123, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:12311:20781:15493 1:N:0:GATCAG merged offset:40 overlap:110 diff:0
CACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCA
-
AAAAAEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEESe`eeeeeZeie`e`Siiieeiieeeaiii`iiSeieieeeiiiSiSiieeiiie eiiiieiSieiiiiZieiieiiiiiaea `Sii `iSe`eiiieeeieSZe`eiee`EEEEE EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA
8, pos: 121, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:13212:8855:14707 1:N:0:GATCAG merged offset:23 overlap:128 diff:0
CCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGC
-
AAAAAEEEEEE6EEEE6EEEEEEVai`e`SeieiieeiiieSiiiei\e`eiiiiiieiiiiiSiiiiieiiieieieiiiiSiieiea`iiS `iSW`SeSie`i`iiiiSi``ieiei`i iSiS iiiiiieeiiSaeei`iiSeSiZe``EE EEEEEEEEEEEEEEEEAAAAA
9, pos: 120, distance: 1, forward
@NB551106:9:H5Y5GBGX2:1:12107:16190:15233 2:N:0:GATCAG
CCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAACGCCAACAAGGAAATCC 
+
6A6A/A//EAEEEE6EE//E6EEA/AE//EEA///6EEE///EAE//EEE//AA/</EE/6E6/6EAE/6/EAE///EEEEA/EA<EE/EEE AEEAAAEA<A/////<A//E/<EE//// /<// <E/E66/<A//<////A//EE/////6 
10, pos: 110, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:13206:2898:10412 1:N:0:GATCAG merged offset:0 overlap:129 diff:0
GGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCA 
-
\aaaae`iiiSeiiiiiieiiiiiiiiS`iiiiieei`iSiiieiiiiiiiiiiiiiiiiiiiiii`iiieiiiiieiiiee eiiiiiiiiiiiieeiiaiiieiiiiii eiie eiiiii`eiieO\ee 
11, pos: 110, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:13108:15474:2849 1:N:0:GATCAG merged offset:21 overlap:128 diff:0
GGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGCGTGG
-
AAAAAEEEEEEEEEEEEEEEEieii`iSeeeiiieiiieiiiiiiiiiieiiieeiiii`ieeiiiiiiiZiiiieiiiiei iiiiieiiiiiieeii`iiiiiiiiiii iiii iiiiiieeiiS`eeii`iiiiiiiiiii iSiVeSaEEEEEEEEEEEEEEEEAAAAA
12, pos: 110, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:11210:20113:20326 1:N:0:GATCAG merged offset:21 overlap:128 diff:0
GGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGG
-
AAAAAAEEEEEEEEEEE/EEE`ieZeeei`eZiSiSJiiiiiii`ii`iiiS`Se`OeiiiiSieieeeZeieieiiiiSi` ii`iiSeiiSieOeiiJiZeeaieiiii `Sii iiiieee`ieS`e``e`iii`ei`eSe\ eSS``\ZEEEEEEEEEEEEEEEEAAAAA
13, pos: 110, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:12306:15839:8991 1:N:0:GATCAG merged offset:21 overlap:128 diff:0
GGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGG
-
AAAAAEEEEEEEEEEEEEEEEeeee``ieeeeiSe``eeiiiiiiiiieiiiiiiiiiiieiiiieeeiiiiiiiiiiiiii iiiiiiiiiiiiiiiieaeeSiiiiiii iiii iiiiieeiiiii`eiieiieeiiiieei `e`e`e`EEEEEEEEEEEEEEEEAAAAA
14, pos: 110, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:22106:2408:9991 1:N:0:GATCAG merged offset:21 overlap:128 diff:1
GGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGG
-
AAAAAEEEEAEEEEEEAEEEEeieiEiSeieiiOSe`SeSi`iiJSeeiSiiiiiZ\e`iiieaii`i\ieiiieiiiiiii Siiieiii`iiieeii`ZeSeiiie`ei e`ee `J`eeSiiSS`SeiSe`ZSSeSZ``eOi ``\J\OZEEEEAEEEE6EEEEEEAAAAA
15, pos: 105, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:13106:22209:19593 1:N:0:GATCAG merged offset:0 overlap:133 diff:0
GCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAA 
-
a\a\eiieeii`SSiiiiiiSiiiSeiSiieiieSiiiiiiiiiei`eieiiiiieiiiieeiiiiiieiieSiiii ii`iiiiieiieiiieiiiieeaiii`i eiSi Si`iiiieiSiiieiiiiiaaV\e 
16, pos: 103, distance: 1, reverse
@NB551106:9:H5Y5GBGX2:1:13304:5888:13157 1:N:0:GATCAG
ATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGGCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGC
-
<E/EEEEE6<</<E/<<<<AEAE<EEEE/EEEEEEA<EEEEAAAEAAEEEEE/<EEEEEAE<EEEEAEEEA<EEE EEEAEEEEEEEEEEEEAEEE/EEEEEEE EEEE EEEEEEAEEEEEEEEEEEEEEEEEEEEE EEEEEEEEEEEAAAAA
17, pos: 103, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:12111:18507:10428 1:N:0:GATCAG
ATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGC
-
/EAE/A/AEE/A<</<<AAE/E<AA</E<EEE<EEEE/EEA/EAAAAEEAEEEA/EEAEAAEAEE/EEEEAEAEE AEEEEEEEEEEEE6EEEEEE/EEEE/AE EEAE EEEEEEEEEEAEEEEEEEEEEEEEEEEE EEEEEEEEEEE/AAAA
18, pos: 102, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:22110:25007:5842 1:N:0:GATCAG merged offset:0 overlap:134 diff:0
TGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT 
+
\aO\V`Zeiiiei``iieiiiiiieiieii`SiiieiiSiiiiiiiiiiiiiii`iiiiiiiiiiiiiiiiiii iiiiiiiiiiiiiieiieeeiiiiiiii i`ei iiiiiieiiSii`ieiiieiiiSeeVO\ 
19, pos: 102, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:12305:9255:3059 1:N:0:GATCAG merged offset:0 overlap:139 diff:0
TGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATG
-
eaaaaiiieeiiiiieiiiieiiiiieiiiiiiiiiiiiiiiiiiieiiiiiiiiiiiiiiiiiiiiiiiiiii iiiiiiiiiiiiiiiiiieiiiiiiiei iiii iiiiieiiiiiiiiiiiiiii`iiiiei eeea\
20, pos: 102, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:13305:13527:11292 1:N:0:GATCAG merged offset:1 overlap:150 diff:0
TGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTT
+
AaeaOii``eieeee`SeiiiiiiiiiiSii`iiiiiiiiiiiiiiiiiiiiiiiiiieiieiiiieiiiie`i iiieeiiiiiiieiiiii`ieiiieiii ieii iiiieieiiiiiiiieiii`ieiiie`e `eiS`SSiiiiii\VaaA
21, pos: 102, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:22109:24401:1453 1:N:0:GATCAG merged offset:1 overlap:150 diff:0
TGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCGGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTT
-
AVaVaSi`eiieeiiiiiii`Seieieeiii`eiiieiiiieiiiiiiiieiiiiieeiiiiiiiiiieeieii iiiiiSiiiiiiiiiiiiiiiieiiiei iiii iSieiee`iiiieeiiiiiieei`eeei `ee``eeiie`eiaaaaA
22, pos: 89, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:22103:7493:13522 1:N:0:GATCAG
CACATTTGAGAGTTAACGTCTTCCTTCTCTCTCTGTCTTAGGGACTCTTGATCCCAGAATG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGG
-
<//A/AEE///<EEEE/<//EA/EEE/E////AEEE6/E6/A/EEAAE/6<E/<<<A/A/E E6<EAA<<E<//EAEEEE/AEAA/EEE/ //// /EEEE/EEEEEE//AA/EA/EEA/E/EE /EEEEEAEE6EAEAEEEAEEEEEAAAAA
23, pos: 89, distance: 1, forward
@NB551106:9:H5Y5GBGX2:1:11207:12649:18883 2:N:0:GATCAG
CACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAACTCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGG
+
AAAAAEEEEEEEEE6/EEEEEAEEEEEEE6EEE6EEEEEEEEEEEEEEEAEAEEEEEEEEE EEEEAEEAE/EEEEEEEEEEEAEAEEEE EE/E <AEEAEEA<E//AAEEEEEE<EE/A/A< //<<<A/AA<//AA<A/AA/A//</A<A//
24, pos: 89, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:12202:5391:17111 2:N:0:GATCAG
CACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGG
+
AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEE EEEEEEEEEEEEEAEEEEEEEEEEEA/E EEE/ /EEAEAEE/E/AEEEEEEE/A/E<AAAE //<6///EA/<A/<<6/AA<EEAE/A/EEA
25, pos: 83, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:21107:2005:9896 2:N:0:GATCAG
TGCCAGTTAACGTCTTACTTCTCTCTCTGTCTTAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCA
-
<E///A/A//A<EAAE/EEEAEAE/EAAE<<</EE/////EEAEAE<E<<EEEEE E/EEAEEAEEEE<EE/AE/E/EEA<A/E AA/E AEEEEAEE<EAEAEE/EEEEEEE/EEEE /AEEEAEEEEAEAEAEEEEEEEEEEEEEEEA6AAA
26, pos: 82, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:11210:9514:13906 2:N:0:GATCAG
GCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATG
+
AAAAAE6/EEEEEEEEEEAEEEEEEEE6EEEAEEEEAEEEEEEEEEEEEEEAEE E6EAEEEEEEEEEEEEEEEAEAAEEAE6 /AE/ EAEE/6EAEEE/E//EA<AAE<A<E/AA E/<E</AE////A<A<<<A//A/A<A/<//////<A/
27, pos: 82, distance: 1, reverse
@NB551106:9:H5Y5GBGX2:1:11311:8139:8774 1:N:0:GATCAG merged offset:71 overlap:80 diff:1
GCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGATAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCAGCTGCTCTGCTCTAGACCCTGCTCATCTCCACA
-
AA/AA/EA/A6/EE/EEEEAEEEEEEE/E/AEEEAEEEEEEEEE/EEE/EE/// /<EE/E/EEEEA/EEEESSSDOO`SESO iSae ie`iiieJ`S`eZ==SSiiOS`e`Sei` i`iSiOQ`SOSJeeVSi`aQeeiie\eJ`OSeia=e`AEEEEAE/AAEEEEEE/EEEEEE/EEEEEEEEE/EE//EAEA/6EEEEEEEEEEEEAEAAEEEEEEA6AAA
28, pos: 82, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:13306:19825:7070 1:N:0:GATCAG merged offset:71 overlap:80 diff:0
GCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCAGCTGCTCTGCTCTAGACCCTGCTCATCTCCACA
-
AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE EEEEEEEEEEEEEAEEE`eZieee``e` eZSe eii`i`Z`Ze`iiiSe``Siie``iS`i Ze\\eS`iiSiiiS``\``e`ieii`eSiaeaiiieeEEAEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA
29, pos: 79, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:21206:9257:20274 1:N:0:GATCAG merged offset:0 overlap:132 diff:0
AGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGC
-
eeaeO`iiSiSiieiiei`SeieieeieiQiZeeiiii`iSiieeeieSei iiSiSiZiiiZiiieeS`Qee`iiieie eeii `S``eSZe`eeiS`eeeeeeeSeSe`S` S`S`SeiS`SS`S`SSaO\\O
30, pos: 79, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:22302:9734:16623 2:N:0:GATCAG
AGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGC
-
A<A/AAA/EE/EE/E/EAEEEEEE</AEEAE//EAAE<<AEEA/EAEEA/E AAAAEAEEEEEEE//EEE<AA<6AEEEE EEEA 6E6AE/AEE/EEEEEEEEE/AEEEEEEE EEEA/EAEE6EEEEEEAAAA/
31, pos: 79, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:12101:16909:12188 2:N:0:GATCAG
AGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGC
-
EA<<<<EE/<<<AAE<AEAEAEEE<EEEEEEAEEEAEEAEEEAEEEEEEEE EEEEEE<<A/EEAEEAAEEEEEEE6EEE EA/E EEEEEEEEE6AAEEEEEEEEAEE/EEEE AEEEEEEEE/EEEEEEAAAAA
32, pos: 79, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:22302:9734:16623 1:N:0:GATCAG
AGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCAGATCGGAAGATCAAACGT
+
A/AAAEAEE/EEAEEEEEAEAEEAAAEAEEEEA6EEE/EAEE/EEEEEAEE EEAEEEEAEEEE6EEE/E/EEEA6AAEE EEEA AE/EE/<6AEEEAEEE<EEEAEEEE<6< 6<EE/</EEEEE6AA/EEEEAEAEEA<<E/AE/EE/E6<<
33, pos: 79, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:12101:16909:12188 1:N:0:GATCAG
AGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCAGATCGGAAGAGCTCACGG
+
A/AAAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEE6EEEAEEEEEE EEEEEEEEEEEEEEEEAEEEE<AA6EEE AEEE EAEEAEEE//<EEAEEEAEEAA//EEAE EEEEEEE//EEEEE<AE<AEEEE/<<AAEE/E<A//<<A/
34, pos: 76, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:12204:16446:13427 1:N:0:GATCAG merged offset:0 overlap:127 diff:0
TAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTT
-
ea\eeiiiiiiiiiiiiiieiiiiiieiiiiiiiiieeiiiiiiiiii iiiiiiiiiiiiiiiiiiiiiiiiiiii iiii iiiiiiiiiiiiiiiiiiiiiii`ieei iieiiiieiZeiiiee\a\
35, pos: 76, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:12206:3492:9156 1:N:0:GATCAG
TAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTA
-
EEEEE/EEEEEEEEEEEE/EEEEEE<EAAEEEEEEEEEEEEEEEEEEE EEEEEEEEEEEEEEEEEEEEEEEEEEEE EEEE EEEEEEEEEEEEEEEEEEEEEEEEEEEE EEEEEEEEEEEEEEAAAAA
36, pos: 76, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:12206:3492:9156 2:N:0:GATCAG
TAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTT
+
AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE EEEEEEEEEE/EEEEEEEEEAEEEEEEE EEE6 EEEEEEEAEEEEEEEAEEEEEEEEEEEE EEAE<EEEEAEEE/AEEAE
37, pos: 76, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:21211:17320:5563 1:N:0:GATCAG merged offset:0 overlap:127 diff:0
TAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTT
-
aeaeeieeiiie`iieeiiiiiiiiiieiiieSiieeeiiieiiieii eie`iiiiiiiiiiii`iiieiiiiiii aiii iiiiiiieiiiiiiiiiiiiieii`iii iiiiiiiiiZ`ee`\aeae
38, pos: 76, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:22108:26312:10622 1:N:0:GATCAG merged offset:29 overlap:122 diff:0
TAACGTCTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTG
-
AAAAAEEEEEEEEEEEEEEEEEEEEEEEEiieee`e``iee`Se`i`e ieie`Siiii`iS`iSiieeieeiieii ii`` iiSiiieiiSeieieSiieiiieeeiii iiia`iiiiiaeiieie`e`````ZSiieeeOiiiSSeieZieEEEEEEEEEEEEEEEEEEEEEEEEAAAAA
39, pos: 62, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:21206:25614:14503 1:N:0:GATCAG merged offset:0 overlap:117 diff:0
TCTCTCTGTCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTG
-
eeeeeiiiiiiiZi`iiiiiiiiiiiiiiiia`i iiiiiiiiiiiiiiiiiiSiiZ``iiie iiii ieiiieeiiiieeiiiiiiiiiiiiiii iiiiieiiiieiiiiiieeeeee
40, pos: 54, distance: 1, forward
@NB551106:9:H5Y5GBGX2:1:13202:3778:18913 1:N:0:GATCAG
TCATAGGGACTCTGGATCCCAGAAGG TGAGAAAGTTAAAATTACCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGTGGTCCATGGCTC
+
/AAAAEEE/EAEEAAEAEEE/AEE/E E6E6EEEEAEE/EEEE/EEAAAAA/EEE /EE/ E/EE//A/EEA/EEEEEEEE6A////<E E<<///</EE</EE/6<///A////AE/AE6<///E/AE/A
41, pos: 35, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:21108:9888:4646 1:N:0:GATCAG
CAGAAGG TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGAGAGTTTCTGCTTTGCTGTGTGTGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCAGCTGCTC
+
AA6AA<6 /A/AEEEA6A/AAEEE/E//EEE/<A<E EAAE EEEE/EE/EEA/EAEAEEE6AEEE/6E/ E/EE//AE/EEEE/EE//EAEE/EE/A/EA/EEAAA//E/</E//AEEAAAE</A/E<E/AAEAAE//AA//AEAE</AEEA
42, pos: 28, distance: 1, forward
@NB551106:9:H5Y5GBGX2:1:22109:24061:12989 1:N:0:GATCAG
 TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCAAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGAGTGGGGGTCCATGGCTCTGCACCTCAGGCCCA
+
 AAAA<EEEE/AEEEEAEEAAE/EEE6EA AEEE EEEEEEE</EEEE/EEEEEEAEE/EA6E EAE/EEEEEEAE<A<AEAAEEEA//EA/AEE/A/AEE<<EEE//A<EEEEEE6A/6
43, pos: 28, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:13202:7218:7375 1:N:0:GATCAG merged offset:0 overlap:116 diff:0
 TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCA
-
 e=eae`iieiiieeSSieeSiiiiiiei e`i` iSJieaii`iSiiiiSiiiiSSiOiiii iSiiO=iiiiiZiieiiiiiVieiiiiiii`Siiiiaiieiii=ieiiieeeeSae
44, pos: 28, distance: 1, reverse
@NB551106:9:H5Y5GBGX2:1:22109:24061:12989 2:N:0:GATCAG
 TGAGAAAGTTAAAATTCCCGTCGATATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCA
-
 A<<6<<EEEEAEE/AE<//<EEE/EAAA <AEA EEE/EE/EE//EEE/EE/EEE///E/EE AA/AA/EEE/AAEEE/EEEEEEEEEEEEAEEEEEEEEA/AEEEEEEAEEEEAA//A
45, pos: 28, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:12312:12247:11795 1:N:0:GATCAG
 TGAGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCAACCCTATTCTCATGACTGGCAGATTCTCTCCTCT
+
 AA6A6EE6E/EE66EEE/AEEA/E/EA/ /E/E /E/EE//EE/////EEEE//EAAE/<EE E/E//E/E/A<E///EE/E</////E/E///EEA/EA//<6//EEAE/////////AA///EAA<<<<//</</EE/6/</<///A//
46, pos: 26, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:21205:17687:9844 1:N:0:GATCAG merged offset:35 overlap:116 diff:0
 AGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCAGCTGCTCTGCTCTAGACCCTGCTCATCTCCACATCCTAAATGTTCACTTTC
+
 AAAAAEEEEEEEEEEEEEEEEEEEEE EEEE EEEEE`iieeeieeSi``iie`e`eeei eee`eiiiiiSSiiii`eiiiZeSeiSiiii`iiieii`SiiiSJ`iii`iii`iSiiS`ei`iie``OeiiiiiiiiiiJZeeS\e`SeSi`EEEEAEEEEEEEEEEEEEEEEEEEEEEEAAAAA
47, pos: 26, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:13302:10944:2114 1:N:0:GATCAG merged offset:35 overlap:116 diff:0
 AGAAAGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCAGCTGCTCTGCTCTAGACCCTGCTCATCTCCACATCCTAAATGTTCACTTTC
+
 AAAAAEEEEEEEEEEEEEEEEEEEEE EEEE EEEEE`eeZ``e``Z`Z``eZZ`Sieei `ee`i`iieSiiaeiiiieiiiiiieiiiiieeiieiieeaaiSOei`ieiiii`Se`iee`eiSe`ieSiie`Sii`eee````SZZe`Z`ZEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA
48, pos: 22, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:12211:24962:16940 1:N:0:GATCAG merged offset:31 overlap:120 diff:1
 AGTTAAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCAGCTGCTCTGCTCTAGACCCTGCTCATCTCCACATCCTAAATGTTCACTTTCTA
+
 AAAAAEEEEEEEEEEEEEEEEE EEEE EEEEEiSieSSieeSSZS`eeeSSeSe\ ieeeiea``ZSE`SieOiiiiii`iSeiieeeeiieiiiOiaiSaiiieaeiiOiSSieeeeeee`iSeeieiiSe`ee`````e=ieeSiiSieSSEEEEEEEEEEEEEEEEEEE6EAEEEEAAAAA
49, pos: 18, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:21111:2651:10876 1:N:0:GATCAG
 AAAATTCCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCAGCTGCTCTGCTCTCGACGCTGCTCAT
+
 AAAAAEEEAEEEEEEEEE EEEE EEEEEEEEEEAEEEEEEEEEEEEEEEEE EEEEEEEEEE/EEEEEEEEEEAEEEEAEEEEEE6EAAEEEEEE//E/EE/E/E6A/A<EAEEEEEEEAE</</A/<<AE/6EE/A<<A///</</6AAA<<
50, pos: 12, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:22308:19431:1802 1:N:0:GATCAG merged offset:0 overlap:131 diff:1
 CCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCAGCTGCTCTGCTC
+
 \aeOaeiaeSi` `eS` ``Seiei\iJEeiiiSeSSSieSi`iii ieSSeSeiaSSiiiiiSiiieei=iOeeiiVeieSieeiieie`eieiieiiOi`eiOiSieOeeiiSS`iieaSiiii`OZeaa\\
51, pos: 12, distance: 0, forward
@NB551106:9:H5Y5GBGX2:1:12201:2567:10967 1:N:0:GATCAG
 CCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCCGCTGCTCTGCTC
+
 AAAAAEEEEEEE EEEE EEEEEEEEAEEEEEEEEEEEEEEEEEEE EEEEEE6EEAEEEEEEAEEEE/EE/AEEAE/EEAEE/AEEA/EEAAEEEE/EEEE/EEA/6EEEEEAEEAEEEE//AEEEEE/EEAA
52, pos: 12, distance: 0, reverse
@NB551106:9:H5Y5GBGX2:1:12201:2567:10967 2:N:0:GATCAG
 CCCGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGAAATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCAGCTGCTCTGCTC
-
 /A/E/<E<A<AA EE/E E/EE/AEAEE<EEE</EAEEEE</<E/E EEEEE6AEE/</EEEEEAEEA/EEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEE6EEE/EAEEE/EEEEEEAAAAAA
53, pos: 12, distance: 2, reverse
@NB551106:9:H5Y5GBGX2:1:21108:9888:4646 2:N:0:GATCAG
 CACGTCGCTATC AAAA CATCTCCGAAAGCCAACAAGGATATCCT CGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGGCTCTGAACCTCAGGCCCACCTTTTCTCATGTCTGGCAGCTGCTCTGCTCTAGACCCTGCTCATCTCCAC
-
 </<6</<//AE/ <A// /<EAEE/<E/EE<A/E///////EEEEE EE<////<E/E/E/EE<E/<EA6//EE/E/</E</E<EEEEA/A/EEEEAE/EEEE66EEEEEAEEEEE//E/AE<EEE6EEE//EEEEEE/EEEA6EEEEEAA6A/

./mutscan -1 R1.fq.gz -2 R2.fq.gz 
Mutscan v1.14.0, time used: 28 seconds
zlangley commented 5 years ago

I am just running it on the files in the testdata directory, R1.fq.gz and R2.fq.gz, which are indeed small. However, I also see the same output on some of my own data, which runs for 49 seconds. I am sure the mutations are there because I can find them with fgrep.

sfchen commented 5 years ago

What are the mutations in your own data?

Probably it's not included in the built-in targets.

zlangley commented 5 years ago

I was providing my own mutation, but I just realized my definition for R was wrong. It seems to be working now, thanks. I would suggest fixing the data in the testdata folder to output something as well though, as this suggested to me the problem was not on my end.