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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,661,508 |
T→G |
T250P (ACC→CCC) |
hcaR ← |
DNA‑binding transcriptional regulator HcaR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,661,508 | 0 | T | G | 86.2%
| 79.8
/ 5.9
| 29 | T250P (ACC→CCC) | hcaR | DNA‑binding transcriptional regulator HcaR |
| Reads supporting (aligned to +/- strand): ref base T (1/3); new base G (13/12); total (14/15) |
| Fisher's exact test for biased strand distribution p-value = 5.98e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01 |
GCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTG > NZ_CP009273/2661420‑2661591
|
gCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTa > 1:402066/1‑90 (MQ=255)
tCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAat < 1:2634/90‑1 (MQ=255)
cATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAatt > 2:116953/1‑90 (MQ=255)
aTCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAatta < 1:116953/90‑1 (MQ=255)
aTCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAatta < 2:368548/90‑1 (MQ=255)
tctcCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAattat < 1:677276/90‑1 (MQ=255)
tcCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTc < 2:525943/90‑1 (MQ=255)
ttcttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATaa > 2:682981/1‑90 (MQ=255)
tcttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAAc < 2:329753/90‑1 (MQ=255)
ttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCg < 2:597733/90‑1 (MQ=255)
aCGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTa > 2:35875/1‑90 (MQ=255)
ccATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCa > 1:276320/1‑90 (MQ=255)
ccATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCa > 1:745044/1‑90 (MQ=255)
aTCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCaaa > 1:148836/1‑90 (MQ=255)
gTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGa < 1:490837/90‑1 (MQ=255)
gTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGa < 1:607900/90‑1 (MQ=255)
aaaGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACg > 2:634190/1‑90 (MQ=255)
gCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGccc < 1:621182/90‑1 (MQ=255)
gCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGccc < 2:210555/90‑1 (MQ=255)
gCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCAGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGccc < 2:348752/90‑1 (MQ=255)
aTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGc > 1:676188/1‑90 (MQ=255)
aTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGc > 1:358842/1‑90 (MQ=255)
aTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGc > 1:178542/1‑90 (MQ=255)
aGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCAt < 1:682981/90‑1 (MQ=255)
aGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCAt < 2:470372/90‑1 (MQ=255)
gCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGc > 1:213422/1‑90 (MQ=255)
tttCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacc > 1:683959/1‑90 (MQ=255)
ggCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGAtt > 2:428219/1‑90 (MQ=255)
gTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTg < 1:703918/90‑1 (MQ=255)
|
GCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTG > NZ_CP009273/2661420‑2661591
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
ATCGCGTAATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGACGATATT > NZ_CP009273/2661410‑2661607
|
ATCGCGTAATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTA > SRR3722079.405465/1‑100 (MQ=60)
TCGCGTAATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGAT < SRR3722079.276011/100‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacagCGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAA < SRR3722079.730952/70‑1 (MQ=60)
ctggtctcgtgggctcggagatgtgtataagagacagGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAAT < SRR3722079.312233/63‑1 (MQ=60)
TCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATA < SRR3722079.2655/100‑1 (MQ=60)
ATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAAC < SRR3722079.117917/100‑1 (MQ=60)
TCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACC < SRR3722079.684384/100‑1 (MQ=60)
TTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCA > SRR3722079.753004/1‑100 (MQ=60)
TTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCA > SRR3722079.278630/1‑100 (MQ=60)
CTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAA > SRR3722079.150121/1‑100 (MQ=60)
CAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGC > SRR3722079.683283/1‑100 (MQ=60)
CAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGC > SRR3722079.361650/1‑100 (MQ=60)
CAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGC > SRR3722079.180101/1‑100 (MQ=60)
GTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCC < SRR3722079.495160/100‑1 (MQ=60)
GTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCC < SRR3722079.614031/100‑1 (MQ=60)
GCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGC < SRR3722079.627505/100‑1 (MQ=60)
GCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGC > SRR3722079.215245/1‑100 (MQ=60)
GGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACC > SRR3722079.691150/1‑100 (MQ=60)
AGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGA < SRR3722079.690156/100‑1 (MQ=60)
GTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGAC < SRR3722079.711381/100‑1 (MQ=60)
GATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGACGATATT > SRR3722079.647179/1‑100 (MQ=60)
|
ATCGCGTAATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGACGATATT > NZ_CP009273/2661410‑2661607
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
