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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,202,478 |
T→G |
Y345D (TAT→GAT) |
yehP → |
VWA domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,202,478 | 0 | T | G | 97.9%
| 150.2
/ NA
| 48 | Y345D (TAT→GAT) | yehP | VWA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/1); major base G (28/18); minor base A (1/0); total (29/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGC > NZ_CP009273/2202392‑2202563
|
tACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATg < 1:139357/90‑1 (MQ=255)
tGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGAcc < 1:499045/90‑1 (MQ=255)
gACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACcg > 2:1360581/1‑90 (MQ=255)
gCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGa > 1:216401/1‑90 (MQ=255)
cATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGAt < 1:1418868/90‑1 (MQ=255)
aTCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGAt > 2:1512593/1‑89 (MQ=255)
aTCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGAt < 1:1512593/89‑1 (MQ=255)
aTCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATa > 2:1334643/1‑90 (MQ=255)
aTCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATa > 2:837150/1‑90 (MQ=255)
aTCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATa > 2:195270/1‑90 (MQ=255)
tGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGccc < 1:1475427/90‑1 (MQ=255)
gAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATAc < 2:41266/84‑1 (MQ=255)
gAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATAc > 1:41266/1‑84 (MQ=255)
aaGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGgcg < 2:671102/90‑1 (MQ=255)
aGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGgcgc < 1:623394/90‑1 (MQ=255)
aGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGgcgc < 1:450702/90‑1 (MQ=255)
tgtgtCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATAc > 2:38519/1‑77 (MQ=255)
tgtgtCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATAc < 1:38519/77‑1 (MQ=255)
tgtgtCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTg > 1:1343770/1‑90 (MQ=255)
gagCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGt > 2:864561/1‑90 (MQ=255)
gCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGgcg > 2:1309996/1‑90 (MQ=255)
gCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCAATGACCGCGATACGGCCCAGCCGCTGGTTAATTTCGgcg > 2:701088/1‑90 (MQ=255)
cATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGgcgc < 1:204992/90‑1 (MQ=255)
aGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAAt < 1:837150/90‑1 (MQ=255)
cTGGGACTGGCAGCGCTCGATAGCACCGCAACCCCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAgcc < 1:264910/90‑1 (MQ=255)
gACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCa > 2:1285398/1‑90 (MQ=255)
tGGCAGCGCTCGATAGCACCGCAACACCTTGCGATg > 1:1494103/1‑36 (MQ=255)
tGGCAGCGCTCGATAGCACCGCAACACCTTGCGATg < 2:1494103/36‑1 (MQ=255)
tGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGa > 1:473241/1‑90 (MQ=255)
tGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGa > 1:180578/1‑90 (MQ=255)
tGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGa > 2:1541552/1‑90 (MQ=255)
cAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGc < 2:953260/90‑1 (MQ=255)
aGCGCTCGATAGCACCGCAACCCCTTGCGATGCCCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGcc < 1:1046970/90‑1 (MQ=255)
gcTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAgcc < 2:311739/76‑1 (MQ=255)
gcTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAgcc > 1:311739/1‑76 (MQ=255)
aGCCCCGCAACCCCTTGCGATGACCGCGATACGGCCCGGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTg < 1:864561/90‑1 (MQ=255)
ccGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGcat > 1:355932/1‑90 (MQ=255)
ccGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGcat > 1:1260328/1‑90 (MQ=255)
ccGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGcat > 1:1155923/1‑90 (MQ=255)
gCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGcatca > 1:704291/1‑90 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGcatca < 1:70355/82‑1 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGcatca > 2:70355/1‑82 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGc > 2:1423627/1‑90 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGc > 2:1141491/1‑90 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGc > 2:444133/1‑90 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGc > 2:817353/1‑90 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGc > 1:1165893/1‑90 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGc > 2:892893/1‑90 (MQ=255)
|
TACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGC > NZ_CP009273/2202392‑2202563
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ 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
TTCATCATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGGAGAATCTTCA > NZ_CP009273/2202381‑2202575
|
TTCATCATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGAT < SRR3722078.1102611/100‑1 (MQ=60)
CATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGA > SRR3722078.219027/1‑100 (MQ=60)
TACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATAC < SRR3722078.140981/100‑1 (MQ=60)
TGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGC < SRR3722078.504952/100‑1 (MQ=60)
CGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCA > SRR3722078.41756/1‑100 (MQ=60)
CATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGG < SRR3722078.1441909/100‑1 (MQ=60)
CATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGG < SRR3722078.1537263/100‑1 (MQ=60)
cagGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCG < SRR3722078.38982/97‑1 (MQ=60)
GGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTG > SRR3722078.1365339/1‑100 (MQ=60)
TGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGT < SRR3722078.1499497/100‑1 (MQ=60)
AGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGT < SRR3722078.630576/100‑1 (MQ=60)
AGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGT < SRR3722078.456084/100‑1 (MQ=60)
CATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCC < SRR3722078.207466/100‑1 (MQ=60)
AGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATG < SRR3722078.848290/100‑1 (MQ=60)
GTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACctttctcttatacacatctgacgctgcggacgatggcgggcgtg > SRR3722078.1518463/1‑56 (MQ=60)
GTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGA > SRR3722078.182705/1‑100 (MQ=60)
GTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGA > SRR3722078.478854/1‑100 (MQ=60)
CTGGGACTGGCAGCGCTCGATAGCACCGCAACCCCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGC < SRR3722078.268148/100‑1 (MQ=60)
GACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCtgt > SRR3722078.315558/1‑97 (MQ=60)
AGCGCTCGATAGCACCGCAACCCCTTGCGATGCCCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTG < SRR3722078.1062637/100‑1 (MQ=60)
CTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCAT > SRR3722078.360273/1‑100 (MQ=60)
CTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCAT > SRR3722078.1280307/1‑100 (MQ=60)
CTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCAT > SRR3722078.1173792/1‑100 (MQ=60)
CGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCA > SRR3722078.712799/1‑100 (MQ=60)
AGCCCCGCAACCCCTTGCGATGACCGCGATACGGCCCGGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGC < SRR3722078.876134/100‑1 (MQ=60)
CCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGC > SRR3722078.1184001/1‑100 (MQ=60)
GCAACCCCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGG < SRR3722078.71180/100‑1 (MQ=60)
ACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGGAGAAT > SRR3722078.345917/1‑100 (MQ=60)
GCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGGAGAATCTTCA > SRR3722078.159934/1‑100 (MQ=60)
|
TTCATCATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGGAGAATCTTCA > NZ_CP009273/2202381‑2202575
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
