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 |
|
A2 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,011,234 |
A→G |
41.1% |
H221R (CAC→CGC) |
rstB → |
sensory histidine kinase in two‑component regulatory system with RstA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,011,234 | 0 | A | G | 41.1%
| 38.3
/ 91.1
| 73 | H221R (CAC→CGC) | rstB | sensory histidine kinase in two‑component regulatory system with RstA |
| Reads supporting (aligned to +/- strand): ref base A (21/22); new base G (13/17); total (34/39) |
| Fisher's exact test for biased strand distribution p-value = 8.12e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.73e-01 |
TAACCAGATGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATAACCTGAGCGCCGCCGAA > minE/1011166‑1011304
|
tAACCAGATGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCAc > 1:3972982/1‑70 (MQ=255)
tAACCAGATGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCAc > 1:1022865/1‑70 (MQ=255)
tAACCAGATGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCAc > 1:1436302/1‑70 (MQ=255)
aaCCAGATGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTcgcg < 1:323642/70‑1 (MQ=255)
ccAGATGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGaa > 1:889393/1‑70 (MQ=255)
ccAGATGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAAc > 1:2538121/1‑71 (MQ=255)
ccAGATGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAAc > 1:1676967/1‑71 (MQ=255)
aTGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCg < 1:3331285/71‑1 (MQ=255)
aTGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCg < 1:2385770/71‑1 (MQ=255)
aTGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCg < 1:4236822/71‑1 (MQ=255)
aTGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCg < 1:2880036/71‑1 (MQ=255)
tGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCTCTCGCGAACTGc > 1:160628/1‑69 (MQ=255)
ggCTGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGaa > 1:1264640/1‑71 (MQ=255)
ggCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGaa > 1:775631/1‑64 (MQ=255)
ggCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGaa > 1:3819414/1‑71 (MQ=255)
ggCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGaa > 1:1762477/1‑71 (MQ=255)
cGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAaca > 1:2055656/1‑71 (MQ=255)
aCAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGaa > 1:1138136/1‑59 (MQ=255)
cAATATCACCGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGt < 1:378067/71‑1 (MQ=255)
cAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGt > 1:1741121/1‑71 (MQ=255)
cAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGt > 1:1283938/1‑71 (MQ=255)
cAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGt < 1:3715237/71‑1 (MQ=255)
atatCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTa < 1:2149512/71‑1 (MQ=255)
tatCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCg < 1:4017460/60‑1 (MQ=255)
aaCGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTgcg < 1:915230/71‑1 (MQ=255)
aaCGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTgcg < 1:963155/71‑1 (MQ=255)
aaCGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTgcg > 1:2163066/1‑71 (MQ=255)
aaCGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTgcg > 1:2158047/1‑71 (MQ=255)
ttAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCg > 1:3031233/1‑71 (MQ=255)
ttAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACg < 1:3533898/43‑1 (MQ=255)
ttAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACg < 1:4041936/43‑1 (MQ=255)
ttAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACg < 1:4123255/43‑1 (MQ=255)
ttAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGtt < 1:1427295/59‑1 (MQ=255)
ttAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGtt < 1:1456915/59‑1 (MQ=255)
tAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGt > 1:883979/1‑71 (MQ=255)
tAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGt > 1:2956684/1‑71 (MQ=255)
aaTTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAg > 1:1206820/1‑59 (MQ=255)
aaTTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAg > 1:581391/1‑59 (MQ=255)
aaTTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAg > 1:1770854/1‑59 (MQ=255)
aaTTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGt > 1:2054374/1‑70 (MQ=255)
aTTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGtt < 1:1762692/70‑1 (MQ=255)
aTTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGtt < 1:3752843/70‑1 (MQ=255)
aTTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGTTa < 1:464071/71‑1 (MQ=255)
ttGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGaa < 1:582205/48‑1 (MQ=255)
ttGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGtt < 1:1750234/69‑1 (MQ=255)
gCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATc < 1:688137/70‑1 (MQ=255)
gCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATc < 1:218935/70‑1 (MQ=255)
gCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATc < 1:591522/70‑1 (MQ=255)
gCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATc < 1:1366622/70‑1 (MQ=255)
gCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATc < 1:2009870/70‑1 (MQ=255)
gCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATc < 1:909339/70‑1 (MQ=255)
gCCAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATc < 1:1311828/70‑1 (MQ=255)
gCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAaca > 1:3286835/1‑48 (MQ=255)
gCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAaca > 1:792655/1‑48 (MQ=255)
gCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAaca > 1:2629235/1‑48 (MQ=255)
cAGCAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGtt < 1:2196885/65‑1 (MQ=255)
cAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTgg < 1:3831325/71‑1 (MQ=255)
cAAAAAACAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTgg < 1:779169/71‑1 (MQ=255)
aaaCAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGAt < 1:446825/71‑1 (MQ=255)
aaaCAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGAt < 1:1190927/71‑1 (MQ=255)
aaaCAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGAt < 1:2600536/71‑1 (MQ=255)
aaaCAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTAgatct > 1:665735/1‑68 (MQ=255)
aaCAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGAt > 1:3698239/1‑70 (MQ=255)
aaCAGCTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGAt > 1:3252622/1‑70 (MQ=255)
cTTATTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGa < 1:3594601/57‑1 (MQ=255)
aTTGACGGTATCGCTCGCGAACTTCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATa < 1:961672/70‑1 (MQ=255)
aTTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATa < 1:2963176/70‑1 (MQ=255)
aTTGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATa < 1:901414/70‑1 (MQ=255)
tGACGGTATCGCTCGCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATAAcc > 1:1751785/1‑71 (MQ=255)
tATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATAACCTGAgcg < 1:4135219/71‑1 (MQ=255)
gCTCACGAACTGCGAACACCGTTAGTGCGCCTCCGTTATCGACTGGAGATGAGCGATAACCTGAgcg < 1:3902155/67‑1 (MQ=255)
cACGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATAACCTGAGCGccgccg > 1:3119733/1‑70 (MQ=255)
cACGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATAACCTGAGCGccgccg > 1:3108903/1‑70 (MQ=255)
cACGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATAACCTGAGCGccgccg > 1:2577249/1‑70 (MQ=255)
aCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATAACCTGAGCgccgcc > 1:3028720/1‑68 (MQ=255)
aCGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATAACCTGAGCGCCGCCGaa > 1:187757/1‑71 (MQ=255)
|
TAACCAGATGGCGGACAATATCAACGCCTTAATTGCCAGCAAAAAACAGCTTATTGACGGTATCGCTCACGAACTGCGAACACCGTTAGTGCGCCTGCGTTATCGACTGGAGATGAGCGATAACCTGAGCGCCGCCGAA > minE/1011166‑1011304
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
