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 |
2,636,526 |
C→T |
100% |
L261L (CTG→CTA) |
yfgL ← |
protein assembly complex, lipoprotein component |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,636,526 | 0 | C | T | 84.4%
| 156.1
/ 22.2
| 64 | L261L (CTG→CTA) | yfgL | protein assembly complex, lipoprotein component |
| Reads supporting (aligned to +/- strand): ref base C (10/0); new base T (36/18); total (46/18) |
| Fisher's exact test for biased strand distribution p-value = 5.04e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.49e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGTTTCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACGGTCAATTT > W3110S.gb/2636467‑2636590
|
cgTTTCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaac < 1:718714/71‑1 (MQ=255)
cgTTTCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaac < 1:2802878/71‑1 (MQ=255)
aTCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTaac < 1:3002869/71‑1 (MQ=255)
aTCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTaa > 1:822973/1‑70 (MQ=255)
aTCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTaa > 1:2728309/1‑70 (MQ=255)
aTCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTaa > 1:1944742/1‑70 (MQ=255)
aTCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTaa > 1:1541569/1‑70 (MQ=255)
aTCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTaa > 1:1686610/1‑70 (MQ=255)
cTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTaacaa > 1:1158571/1‑71 (MQ=255)
cTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTaacaa > 1:2259676/1‑71 (MQ=255)
cTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTaacaa > 1:1909598/1‑71 (MQ=255)
cTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTaacaa > 1:1822478/1‑71 (MQ=255)
cACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaac < 1:1103225/52‑1 (MQ=255)
cTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaacaa > 1:3037319/1‑52 (MQ=255)
cTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAacgac < 1:3434005/68‑1 (MQ=255)
tGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAaac > 1:2474131/1‑49 (MQ=255)
tGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACgg > 1:1717135/1‑69 (MQ=255)
tGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACgg > 1:710103/1‑69 (MQ=255)
tGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACgg > 1:2753939/1‑69 (MQ=255)
cgcAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGt > 1:726917/1‑71 (MQ=255)
cAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGTGAGTCg < 1:2831276/71‑1 (MQ=255)
cAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCg < 1:239262/71‑1 (MQ=255)
aGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCg < 1:2507163/70‑1 (MQ=255)
aTCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaac < 1:3180064/42‑1 (MQ=255)
aTCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaac < 1:3461525/42‑1 (MQ=255)
aTCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaac < 1:201659/42‑1 (MQ=255)
tCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTc < 1:2195134/71‑1 (MQ=255)
cAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCgtg > 1:2209201/1‑68 (MQ=255)
cAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTc > 1:1517053/1‑70 (MQ=255)
cAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTc > 1:1211704/1‑70 (MQ=255)
cAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTc > 1:3608948/1‑70 (MQ=255)
cAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTc > 1:1840305/1‑70 (MQ=255)
gTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACgg < 1:3082093/52‑1 (MQ=255)
gTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACgg < 1:2464352/52‑1 (MQ=255)
gTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACgg < 1:2695525/52‑1 (MQ=255)
cAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAacga > 1:1087577/1‑47 (MQ=255)
cAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACAtag > 1:2080444/1‑65 (MQ=255)
cAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCg > 1:2177458/1‑67 (MQ=255)
cAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGc > 1:3724036/1‑68 (MQ=255)
ttACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAAc > 1:609718/1‑59 (MQ=255)
ttACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTc > 1:221599/1‑66 (MQ=255)
ttACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACg > 1:1397499/1‑71 (MQ=255)
ttACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACg > 1:754400/1‑71 (MQ=255)
ttACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACg > 1:2969635/1‑71 (MQ=255)
ttACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACg > 1:22797/1‑71 (MQ=255)
ttACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACg > 1:2492366/1‑71 (MQ=255)
ttACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACg > 1:3263109/1‑71 (MQ=255)
ttACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACg > 1:3690949/1‑71 (MQ=255)
ttACCATTAAAGCCTAGCGCGAAAACAACCCCGTTAACAACGACGGGAGTc > 1:2415843/1‑51 (MQ=255)
tACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAAc > 1:795438/1‑58 (MQ=255)
tACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCg > 1:2548640/1‑62 (MQ=255)
tACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACg > 1:2321666/1‑70 (MQ=255)
tACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACg > 1:2361998/1‑70 (MQ=255)
aCCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACg > 1:1526086/1‑69 (MQ=255)
ttATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGTGAGTCGTGTc < 1:257951/50‑1 (MQ=255)
ttATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTc < 1:362829/50‑1 (MQ=255)
ataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGTGAGTCGTGTCAACATCGCTCAGACGGTCAAttt > 1:160208/1‑71 (MQ=255)
ataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCgt > 1:3341889/1‑45 (MQ=255)
ataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGa > 1:804044/1‑61 (MQ=255)
ataGGCTAGCGCGAAAACAACGACGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACGGTCAAttt > 1:1777693/1‑71 (MQ=255)
ataGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCaa > 1:1140695/1‑50 (MQ=255)
ataGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCaa > 1:1277485/1‑50 (MQ=255)
ataGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCaa > 1:784454/1‑50 (MQ=255)
taGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACGGTCAAttt < 1:1875808/70‑1 (MQ=255)
|
CGTTTCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACGGTCAATTT > W3110S.gb/2636467‑2636590
|
| 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
