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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,792,107 |
Δ1 bp |
100% |
coding (315/1320 nt) |
uhpC → |
membrane protein regulates uhpT expression |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,792,107 | 0 | G | . | 75.9%
| 100.3
/ 62.9
| 58 | coding (315/1320 nt) | uhpC | membrane protein regulates uhpT expression |
| Reads supporting (aligned to +/- strand): ref base G (3/11); new base . (28/16); total (31/27) |
| Fisher's exact test for biased strand distribution p-value = 1.21e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.60e-01 |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
TGTCTCCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGCTCTGGGTG > W3110S.gb/3792041‑3792170
|
tGTCTCCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACggcat > 1:2734921/1‑68 (MQ=255)
tGTCTCCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACggcat > 1:2847536/1‑68 (MQ=255)
tGTCTCCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACggcat > 1:3265792/1‑68 (MQ=255)
tGTCTCCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACggcat > 1:3345236/1‑68 (MQ=255)
tctcCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCAt < 1:920260/70‑1 (MQ=255)
tctcCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCAt < 1:2406156/70‑1 (MQ=255)
cGGCATTGTCAGCGATCGCTCATATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCaa < 1:305566/71‑1 (MQ=255)
cGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCaa < 1:2516404/71‑1 (MQ=255)
ttGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCAt < 1:1525164/61‑1 (MQ=255)
ttGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCAt < 1:3652222/61‑1 (MQ=255)
ttGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCAt < 1:2930982/61‑1 (MQ=255)
ttGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCAt < 1:3596194/61‑1 (MQ=255)
ttGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCAt < 1:194431/61‑1 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCt > 1:1089269/1‑71 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCt > 1:264149/1‑70 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg > 1:749584/1‑71 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg > 1:2668314/1‑71 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg > 1:888718/1‑71 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg > 1:231742/1‑71 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg > 1:1271546/1‑71 (MQ=255)
aGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGttt < 1:123472/71‑1 (MQ=255)
aGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGttt < 1:637110/71‑1 (MQ=255)
tCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCt < 1:1855984/71‑1 (MQ=255)
cGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtc > 1:2479014/1‑71 (MQ=255)
cGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtc > 1:3444629/1‑71 (MQ=255)
gCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtct > 1:3075151/1‑71 (MQ=255)
gCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtct > 1:784980/1‑71 (MQ=255)
gCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtct > 1:969914/1‑71 (MQ=255)
cTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc < 1:3249429/71‑1 (MQ=255)
cTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc < 1:347688/71‑1 (MQ=255)
tCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACAt < 1:1920034/55‑1 (MQ=255)
aaaTGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGa < 1:1448965/70‑1 (MQ=255)
aaaTGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGa < 1:1628591/70‑1 (MQ=255)
aaaTGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGa < 1:587571/70‑1 (MQ=255)
aaaTGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGa < 1:583303/70‑1 (MQ=255)
aaaTGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGAc < 1:1637081/71‑1 (MQ=255)
cGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCt < 1:1293773/71‑1 (MQ=255)
ttATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATg > 1:2028979/1‑71 (MQ=255)
aTTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTa > 1:100089/1‑68 (MQ=255)
aTTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTa > 1:491014/1‑68 (MQ=255)
aTTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGc > 1:820458/1‑52 (MQ=255)
aTTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGc > 1:932832/1‑52 (MQ=255)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATg > 1:1196698/1‑66 (MQ=255)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATg > 1:655302/1‑66 (MQ=255)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCg < 1:775463/70‑1 (MQ=255)
tGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGtt < 1:943175/70‑1 (MQ=255)
tGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGtt < 1:2116725/70‑1 (MQ=255)
tAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc < 1:75856/45‑1 (MQ=38)
aGGGCTTTTCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCg > 1:2964771/1‑67 (MQ=255)
aGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCg > 1:2404318/1‑67 (MQ=255)
aGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCg > 1:3542482/1‑67 (MQ=255)
aGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGct > 1:3422890/1‑71 (MQ=255)
gggCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGctc > 1:2316622/1‑71 (MQ=255)
gggCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGctc > 1:1069861/1‑71 (MQ=255)
gggCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGctc > 1:901297/1‑71 (MQ=255)
gggCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGct > 1:2321528/1‑70 (MQ=255)
ggCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGctct < 1:2667075/71‑1 (MQ=255)
ggCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGctcg < 1:3474684/71‑2 (MQ=255)
aTCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGCTCTGGGt > 1:268359/1‑70 (MQ=255)
aTCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGCTCTGGGTg > 1:887345/1‑71 (MQ=255)
aTCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGCTCTGGGTg > 1:550918/1‑71 (MQ=255)
aTCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGCTCTGGGTg > 1:488042/1‑71 (MQ=255)
|
TGTCTCCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGCTCTGGGTG > W3110S.gb/3792041‑3792170
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
