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 |
2,636,526 |
C→T |
75.9% |
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 | 75.9%
| 96.5
/ 32.6
| 54 | L261L (CTG→CTA) | yfgL | protein assembly complex, lipoprotein component |
| Reads supporting (aligned to +/- strand): ref base C (5/8); new base T (21/20); total (26/28) |
| Fisher's exact test for biased strand distribution p-value = 5.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01 |
TCGCGTTTCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACGGTCAATT > W3110S.gb/2636464‑2636589
|
tCGCGTTTCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAgcgc > 1:785990/1‑68 (MQ=255)
tCGCGTTTCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAgcgc > 1:2099610/1‑68 (MQ=255)
cgTTTCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGaa < 1:2985147/68‑1 (MQ=255)
cgTTTCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGaa < 1:2251514/68‑1 (MQ=255)
cgTTTCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGaa < 1:3150132/68‑1 (MQ=255)
tCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaaca < 1:1460233/68‑1 (MQ=255)
tCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaaca < 1:3226133/68‑1 (MQ=255)
tCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAaacaa < 1:2155016/69‑1 (MQ=255)
cacaTAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAaacaa < 1:377774/67‑1 (MQ=255)
aaTCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGtt > 1:2685530/1‑69 (MQ=255)
aaTCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGtt > 1:561083/1‑69 (MQ=255)
cACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGcgcg < 1:2923417/47‑1 (MQ=255)
cACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTaacaac < 1:3711952/67‑1 (MQ=255)
gcgcAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaacaa < 1:856961/50‑1 (MQ=255)
gcgcAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaacaa < 1:1531195/50‑1 (MQ=255)
gcgcAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaacaa < 1:423209/50‑1 (MQ=255)
gcgcAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGtt > 1:2859702/1‑57 (MQ=255)
gcgcAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGtt < 1:2385758/57‑1 (MQ=255)
gcgcAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGtt < 1:2457207/57‑1 (MQ=255)
gcgcAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACggg < 1:759939/69‑1 (MQ=255)
cgcAGATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACggg < 1:3200872/68‑1 (MQ=255)
gATCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAaacaa < 1:3594655/45‑1 (MQ=255)
aTCAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGt < 1:964384/66‑1 (MQ=255)
cAAGCGCCGTCAGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCgtg > 1:1890257/1‑68 (MQ=255)
cAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAacgactg < 1:3429656/60‑3 (MQ=255)
cAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACgg < 1:1063568/60‑1 (MQ=255)
cAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACgg > 1:2032882/1‑60 (MQ=255)
cAAGCGCCGACAGGTTACCATTATAGGCCAGCGCGAAaacaa > 1:48950/1‑42 (MQ=255)
gcgcCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTaac < 1:1515458/49‑1 (MQ=255)
aGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGTGAGTCGTGTCa > 1:1060863/1‑60 (MQ=255)
aGGTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCgt > 1:2237050/1‑56 (MQ=255)
aGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCgtg > 1:781102/1‑57 (MQ=255)
aGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCg > 1:2974145/1‑66 (MQ=255)
gTTACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCa < 1:2942286/68‑1 (MQ=255)
gTTACCATTATAGGCTAGCGCGAAAACAACGACGTTAACAACGACGGGAGTCGTGTCAACATCGCTCa < 1:3475037/68‑1 (MQ=255)
ttACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGa > 1:3070142/1‑69 (MQ=255)
tACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGTGAGTCGTGTCAACATCGCTCAGa < 1:3305410/68‑1 (MQ=255)
tACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCa > 1:1451872/1‑56 (MQ=255)
tACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGTTCAGAc > 1:190564/1‑69 (MQ=255)
tACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGa < 1:1138657/68‑1 (MQ=255)
tACCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGa < 1:2163647/68‑1 (MQ=255)
aCCATTATAGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACg < 1:1026466/69‑1 (MQ=255)
tataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGTGAGTCGTGTCAACAt > 1:3178845/1‑54 (MQ=255)
tataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCaa > 1:752665/1‑51 (MQ=255)
tataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCaa > 1:1894369/1‑51 (MQ=255)
tataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCa > 1:2685809/1‑50 (MQ=255)
tataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACa > 1:1474783/1‑53 (MQ=255)
tataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACAt > 1:1730869/1‑54 (MQ=255)
tataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACAt > 1:1243677/1‑54 (MQ=255)
tataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACAt > 1:722802/1‑54 (MQ=255)
ataGGCTAGCGCGAAAACAACGCCGTTAACAACGCCGGGAGTCGTGTc > 1:2766038/1‑48 (MQ=255)
ataGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTc < 1:3016467/48‑1 (MQ=255)
ataGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCg > 1:2529922/1‑44 (MQ=255)
taGGCTAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACGGTCAAtt > 1:2192894/1‑69 (MQ=255)
|
TCGCGTTTCCACATAATCTGACCACTGCGCAGATCAAGCGCCGTCAGGTTACCATTATAGGCCAGCGCGAAAACAACGCCGTTAACAACGACGGGAGTCGTGTCAACATCGCTCAGACGGTCAATT > W3110S.gb/2636464‑2636589
|
| 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
