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 F21 I0 R2
|
308 |
27.9 |
1975068 |
96.7% |
1909890 |
67.2 |
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 | . | 89.4%
| 148.5
/ 12.6
| 46 | coding (315/1320 nt) | uhpC | membrane protein regulates uhpT expression |
| Reads supporting (aligned to +/- strand): ref base G (4/0); new base . (18/23); total (23/23) |
| Fisher's exact test for biased strand distribution p-value = 4.91e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
GTCTCCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGCTC > W3110S.gb/3792042‑3792164
|
gTCTCCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACggcat < 1:1723768/70‑4 (MQ=255)
gTCTCAGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACggcat < 1:1446732/70‑4 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTa > 1:1856998/1‑60 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTa > 1:1857138/1‑60 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTa > 1:17514/1‑60 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTa > 1:1969498/1‑60 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTa > 1:29371/1‑60 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTa > 1:699473/1‑60 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTa > 1:1067394/1‑60 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg > 1:613160/1‑71 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCC‑CCGGCATTa > 1:1861193/1‑60 (MQ=255)
aTCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg < 1:781420/64‑1 (MQ=255)
aTCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg < 1:874742/64‑1 (MQ=255)
aTCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg < 1:1469588/64‑1 (MQ=255)
aTCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg < 1:1209558/64‑1 (MQ=255)
aTCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg < 1:943663/64‑1 (MQ=255)
aTCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg < 1:961104/64‑1 (MQ=255)
tCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg < 1:973438/63‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:435378/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:1009916/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:1961534/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:878750/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:524843/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:848192/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:78747/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:1498097/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:1046903/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:1085566/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:1279599/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:1625843/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:1691064/71‑1 (MQ=255)
cccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:1781229/71‑1 (MQ=255)
ccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:461407/70‑1 (MQ=255)
ccGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGc < 1:1800044/70‑1 (MQ=255)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGtt > 1:1942984/1‑45 (MQ=38)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGc > 1:288817/1‑49 (MQ=39)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGt > 1:1821026/1‑71 (MQ=255)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGt > 1:949151/1‑71 (MQ=255)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGt > 1:1457739/1‑71 (MQ=255)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGt > 1:1262873/1‑71 (MQ=255)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGt > 1:122581/1‑71 (MQ=255)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGt > 1:1077488/1‑71 (MQ=255)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGt > 1:1066235/1‑71 (MQ=255)
ttATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGt > 1:1801756/1‑71 (MQ=255)
ggCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGctc > 1:1002200/1‑71 (MQ=255)
ggCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGctc > 1:606071/1‑71 (MQ=255)
ggCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGctc > 1:1675722/1‑71 (MQ=255)
ggCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGAGTTTGCCGTGctc > 1:1011500/1‑71 (MQ=255)
|
GTCTCCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGCTC > W3110S.gb/3792042‑3792164
|
| 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
