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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
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 | . | 76.8%
| 93.7
/ 58.5
| 56 | coding (315/1320 nt) | uhpC | membrane protein regulates uhpT expression |
| Reads supporting (aligned to +/- strand): ref base G (4/9); new base . (10/33); total (14/42) |
| Fisher's exact test for biased strand distribution p-value = 7.17e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01 |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
TGTCTCCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGCTCTG > W3110S.gb/3792041‑3792166
|
tGTCTCCGGCATTGTCAGCGATCGCACAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACggg > 1:2386357/1‑69 (MQ=255)
tctcCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATTGGGATAGGGCTTATCGCCACggca < 1:3557115/68‑3 (MQ=255)
tctcCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACggca < 1:41235/68‑3 (MQ=255)
cATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAAc < 1:834080/69‑1 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATc < 1:2659924/62‑1 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATc < 1:3065638/62‑1 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATc < 1:3077617/62‑1 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATc < 1:3114571/62‑1 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATc < 1:2236692/62‑1 (MQ=255)
gTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTAT‑AACATTCt > 1:1166246/1‑69 (MQ=255)
aGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg < 1:988514/68‑1 (MQ=255)
aGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTg < 1:2231336/68‑1 (MQ=255)
aGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGt > 1:1051953/1‑69 (MQ=255)
cGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGt < 1:2102723/68‑1 (MQ=255)
cGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGt < 1:2107170/68‑1 (MQ=255)
aTCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTgg < 1:626791/69‑1 (MQ=255)
cAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc < 1:1515139/69‑1 (MQ=255)
cAAATGCCCGTTATTTTATGGGGATAGGGCTTATAGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc < 1:1017676/69‑1 (MQ=255)
aTGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTtctc < 1:2585334/67‑1 (MQ=255)
aTGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTtctc < 1:1772886/67‑1 (MQ=255)
aTGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGAc < 1:2993441/69‑1 (MQ=255)
tGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGAc > 1:3588727/1‑68 (MQ=255)
tGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACg > 1:831722/1‑69 (MQ=255)
tGCCCGTTATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACg > 1:2206964/1‑69 (MQ=255)
ttATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTa < 1:1104888/69‑1 (MQ=255)
ttATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTa < 1:2385935/69‑1 (MQ=255)
tATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCa < 1:551120/39‑1 (MQ=38)
tATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc > 1:1651436/1‑58 (MQ=255)
tATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc > 1:2291213/1‑58 (MQ=255)
tATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc > 1:2184331/1‑58 (MQ=255)
tATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc < 1:2163998/58‑1 (MQ=255)
tATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc < 1:1753723/58‑1 (MQ=255)
tATTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtct > 1:653297/1‑57 (MQ=255)
tATTTTATGGGGATAGGGATTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc > 1:1920837/1‑58 (MQ=255)
aTTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTAt > 1:2255316/1‑69 (MQ=255)
aTTTTATGGGGATAGGGCTTATCGCCAC‑GTCATTATCaa < 1:3470354/39‑1 (MQ=37)
aTTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCaa < 1:1018050/39‑1 (MQ=38)
aTTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCaa < 1:1285571/39‑1 (MQ=38)
aTTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc < 1:2479085/57‑1 (MQ=255)
aTTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTtctc < 1:723255/57‑1 (MQ=255)
aTTTTATGGGGATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTAt < 1:62691/68‑1 (MQ=255)
gggATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGttt < 1:2830031/69‑1 (MQ=255)
gggATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGttt < 1:2834260/69‑1 (MQ=255)
gggATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGttt < 1:3240770/69‑1 (MQ=255)
gggATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGttt < 1:35216/69‑1 (MQ=255)
gggATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGttt < 1:1611020/69‑1 (MQ=255)
gATAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGc < 1:3431123/68‑1 (MQ=255)
aTAGGGCTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCg < 1:1426867/69‑1 (MQ=255)
tAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGcc > 1:1124954/1‑68 (MQ=255)
cTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGAc < 1:111723/43‑1 (MQ=38)
cTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGAc < 1:1196412/43‑1 (MQ=38)
cTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGAc < 1:1696262/43‑1 (MQ=38)
cTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGAc < 1:1700786/43‑1 (MQ=38)
cTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGAc < 1:1743633/43‑1 (MQ=38)
cTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGAc < 1:2350423/43‑1 (MQ=38)
cTTATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGAc < 1:2486826/43‑1 (MQ=38)
ttATCGCCAC‑GGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGCTCTg < 1:2600699/69‑1 (MQ=255)
cGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTa > 1:147073/1‑46 (MQ=255)
agCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTa > 1:2378145/2‑46 (MQ=255)
|
TGTCTCCGGCATTGTCAGCGATCGCTCAAATGCCCGTTATTTTATGGGGATAGGGCTTATCGCCACGGGCATTATCAACATTCTGTTTGGCTTCTCGACGTCGCTATGGGCGTTTGCCGTGCTCTG > W3110S.gb/3792041‑3792166
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
