Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F2 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,836,838 |
(C)5→4 |
coding (312/1335 nt) |
adeQ ← |
adenine permease AdeQ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,836,834 | 0 | C | . | 97.7%
| 175.3
/ ‑2.0
| 44 | coding (316/1335 nt) | adeQ | adenine permease AdeQ |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base . (16/27); total (16/28) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.17e-01 |
GGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATAC > NZ_CP009273/3836750‑3836923
|
ggATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGccccac > 1:600809/1‑88 (MQ=255)
ggATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGccccac > 2:783866/1‑88 (MQ=255)
ggATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGccccac > 2:567041/1‑88 (MQ=255)
ggATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGccccac > 1:743039/1‑88 (MQ=255)
atcAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTTCGCCCAGCCCGGTCTGCCAGGAGATGCCCACCG‑TCccacgacctcga < 2:469993/88‑1 (MQ=255)
aaCAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCccacgaccacga < 2:889031/90‑1 (MQ=255)
aaCAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCccacgaccacga < 1:567041/90‑1 (MQ=255)
aaCAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCccacgaccacga < 2:343468/90‑1 (MQ=255)
aaCAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCccacgaccacga < 2:741034/90‑1 (MQ=255)
cAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAg < 2:829153/90‑1 (MQ=255)
aGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAgg > 1:713002/1‑90 (MQ=255)
gCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGc > 2:197791/1‑90 (MQ=255)
gCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGc > 1:241464/1‑90 (MQ=255)
gCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGc > 2:348566/1‑90 (MQ=255)
gCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGc > 2:775326/1‑90 (MQ=255)
tGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCaaa > 1:287917/1‑90 (MQ=255)
tGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCaaa > 2:835088/1‑90 (MQ=255)
gCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAaagaa < 2:740637/90‑1 (MQ=255)
aaaaaTAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAgg < 1:835088/90‑1 (MQ=255)
aaaTAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCg > 1:457617/1‑90 (MQ=255)
aGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCa < 1:487712/90‑1 (MQ=255)
aGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCa < 2:713002/90‑1 (MQ=255)
gTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAgg > 2:400296/1‑83 (MQ=255)
gTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAgg < 1:400296/83‑1 (MQ=255)
tCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAg < 1:264838/90‑1 (MQ=255)
tCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGc < 1:815470/90‑1 (MQ=255)
aCTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCa > 2:13613/1‑90 (MQ=255)
gAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGcc < 1:163093/90‑1 (MQ=255)
tGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGcc < 1:503842/90‑1 (MQ=255)
gcgcCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCa < 1:50333/90‑1 (MQ=255)
gcgcCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCa < 1:383657/90‑1 (MQ=255)
gcCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACg > 2:821556/1‑90 (MQ=255)
cccATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACgg > 1:679900/1‑90 (MQ=255)
aTCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTa < 2:477860/90‑1 (MQ=255)
tCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTaa > 1:190225/1‑90 (MQ=255)
tCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTaa < 1:783866/90‑1 (MQ=255)
gTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAg < 2:679900/90‑1 (MQ=255)
tCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGc < 1:253035/90‑1 (MQ=255)
gCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTc < 2:185015/49‑1 (MQ=39)
gCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTc > 1:185015/1‑49 (MQ=39)
cAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAata < 2:203917/90‑1 (MQ=255)
gagaTGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATcc < 1:161543/90‑1 (MQ=255)
gaTGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATcccc < 2:640842/90‑1 (MQ=255)
gaTGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATcccc < 1:251883/90‑1 (MQ=255)
gaTGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATcccc < 1:225968/90‑1 (MQ=255)
aTGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGACCCACCCCCACGGGAAAGTTAGCAAATATcccct > 1:219673/1‑89 (MQ=255)
gCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGc < 2:641401/77‑1 (MQ=255)
gCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGc > 1:641401/1‑77 (MQ=255)
cccccACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATAc < 2:340826/90‑1 (MQ=255)
|
GGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATAC > NZ_CP009273/3836750‑3836923
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAGTACCGGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATAC > NZ_CP009273/3836743‑3836923
|
CAGTACCGGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGAC < SRR3722072.178144/100‑1 (MQ=60)
GATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGG > SRR3722072.725708/1‑100 (MQ=60)
ATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGC > SRR3722072.245511/1‑100 (MQ=60)
CGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAA > SRR3722072.292886/1‑100 (MQ=60)
AACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAA < SRR3722072.577189/100‑1 (MQ=60)
GCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCG > SRR3722072.465996/1‑100 (MQ=60)
AAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCC < SRR3722072.849556/100‑1 (MQ=60)
AAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCC < SRR3722072.407515/100‑1 (MQ=60)
AGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGC < SRR3722072.496528/100‑1 (MQ=60)
TCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCC < SRR3722072.269346/100‑1 (MQ=60)
TCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCG < SRR3722072.829677/100‑1 (MQ=60)
GAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGG > SRR3722072.692063/1‑100 (MQ=60)
GAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGG < SRR3722072.165931/100‑1 (MQ=60)
ataatcggacgtctcgtgggctcggagatgtgtataagagacagCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGG < SRR3722072.364856/56‑1 (MQ=60)
ATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAA > SRR3722072.193526/1‑100 (MQ=60)
TGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGT < SRR3722072.512936/100‑1 (MQ=60)
GCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTT < SRR3722072.390512/100‑1 (MQ=60)
GCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTT < SRR3722072.51256/100‑1 (MQ=60)
ATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCtgtctcttatacacatctccgagcccacga > SRR3722072.188229/1‑70 (MQ=60)
TCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAAT < SRR3722072.797601/100‑1 (MQ=60)
TCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCC < SRR3722072.257321/100‑1 (MQ=60)
CTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGACCCACCCCCACGGGAAAGTTAGCAAATATCCCCT > SRR3722072.223409/1‑100 (MQ=60)
GCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCctg > SRR3722072.652841/1‑97 (MQ=60)
GGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAA > SRR3722072.928494/1‑100 (MQ=60)
GAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAAT < SRR3722072.164357/100‑1 (MQ=60)
GATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATAC < SRR3722072.256145/100‑1 (MQ=60)
GATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATAC < SRR3722072.229788/100‑1 (MQ=60)
|
CAGTACCGGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATAC > NZ_CP009273/3836743‑3836923
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
