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 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,575,785 |
C→T |
40.0% |
A378T (GCT→ACT) |
pqqL ← |
predicted peptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,575,785 | 0 | C | T | 40.0%
| 25.6
/ 43.4
| 40 | A378T (GCT→ACT) | pqqL | predicted peptidase |
| Reads supporting (aligned to +/- strand): ref base C (12/12); new base T (9/7); total (21/19) |
| Fisher's exact test for biased strand distribution p-value = 7.55e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-01 |
AGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATGCATTCGCAGCATCCTGCATATT > W3110S.gb/1575717‑1575851
|
aGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTcagcag < 1:2319030/71‑1 (MQ=255)
cTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGaa < 1:2517466/71‑1 (MQ=255)
aTCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGTAGAAAAAc < 1:1629811/68‑1 (MQ=255)
aTCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCAt > 1:1820086/1‑71 (MQ=255)
gCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGAt > 1:861372/1‑70 (MQ=255)
gCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGAt > 1:178457/1‑70 (MQ=255)
tttttCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGTAGAAAAACCATGCTGATCAAt > 1:2176402/1‑71 (MQ=255)
tttttCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGTAGAAAAACCATGCTGATCAAt > 1:1285941/1‑71 (MQ=255)
tttCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATCaa > 1:2139008/1‑68 (MQ=255)
ttCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGTAGAAAAACCATGCTGATCAATGGt > 1:2312620/1‑71 (MQ=255)
ttCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATCAATgg < 1:1258870/70‑1 (MQ=255)
gCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATCAATGGTTGcc < 1:1059480/71‑1 (MQ=255)
cAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATCAATGGTTGCCaa < 1:1936874/71‑1 (MQ=255)
gTGAGTCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCt < 1:743343/52‑1 (MQ=255)
gTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCt < 1:887174/52‑1 (MQ=255)
gTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCt < 1:2387597/52‑1 (MQ=255)
gAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGTAGaaaaa > 1:1280667/1‑43 (MQ=255)
gAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGa > 1:623992/1‑52 (MQ=255)
gggTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATc < 1:1668543/49‑1 (MQ=255)
gggTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATc < 1:2396206/49‑1 (MQ=255)
gTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCAtt < 1:1830608/69‑1 (MQ=255)
tAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAAt > 1:1334603/1‑71 (MQ=255)
gATTTGACATCATCGAGTTCTTCAGTAGAAAAACCATGCTGATc < 1:1123240/44‑1 (MQ=255)
gATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATg > 1:1554322/1‑70 (MQ=255)
tttGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATCaa > 1:1114384/1‑44 (MQ=255)
tttGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATCAATGGTTGCCAActc > 1:412490/1‑57 (MQ=255)
ttGACATCATCGAGTTCTTCAGTAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATGCAtt > 1:2726931/1‑71 (MQ=255)
aCATCATCGAGTTCTTCAGTAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATGCATTCgc < 1:478283/71‑1 (MQ=255)
catcatCGAGTTCTTCAGTAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATGCATTCgc < 1:1863865/70‑1 (MQ=255)
catcatCGAGTTCTTCAGCAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGc < 1:2182321/55‑1 (MQ=255)
tcatcGAGTTCTTCAGTAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATGCATTCgcag < 1:1847625/70‑1 (MQ=255)
tcatcGAGTTCTTCAGCAGAAAAACCATGCTGATCAATgg > 1:1623756/1‑40 (MQ=255)
atcGAGTTCTTCAGTAGAAAAACCATGCTGATCaa > 1:2029879/1‑35 (MQ=255)
atcGAGTTCTTCAGTAGAAAAACCATGCTGATCaa > 1:2780151/1‑35 (MQ=255)
atcGAGTTCTTCAGTAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATGCATTCGCAGCAt > 1:339608/1‑71 (MQ=255)
atcGAGTTCTTCAGCAGAAAAACCATGCTGATCaa > 1:678516/1‑35 (MQ=255)
atcGAGTTCTTCAGCAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAAt > 1:939531/1‑58 (MQ=255)
gAGTTCTTCAGTAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATGCATTCGCAGCATCCt > 1:222286/1‑71 (MQ=255)
ttcttcAGTAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATg < 1:110095/53‑1 (MQ=255)
ttcttcAGCAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATGCATTCGCAGCATCCTGCa < 1:1690050/71‑1 (MQ=255)
cttcAGTAGAAAAACCATGCTGATCAATGGTTGCCaa < 1:1476675/37‑1 (MQ=255)
cagtagAAAAACCATGCTGAGCAATGGTTGCCAACTCTGCCATTAATGCATTCGCAGCATCCTGCAtatt < 1:122311/70‑1 (MQ=255)
cagctgAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATGCATTCGCAGCATCCTGCAtatt < 1:2733522/70‑1 (MQ=255)
|
AGCTTGCTGATCAACCGCATTTTTCAGCCAGGTGAGGCGGGTAGATTTGACATCATCGAGTTCTTCAGCAGAAAAACCATGCTGATCAATGGTTGCCAACTCTGCCATTAATGCATTCGCAGCATCCTGCATATT > W3110S.gb/1575717‑1575851
|
| 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
