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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
754,163 |
C→G |
46.1% |
R86R (CGG→CGC) |
ycfT ← |
predicted inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 754,163 | 0 | C | G | 46.1%
| 6.9
/ 58.2
| 52 | R86R (CGG→CGC) | ycfT | predicted inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base C (13/15); new base G (16/8); total (29/23) |
| Fisher's exact test for biased strand distribution p-value = 1.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01 |
TCAGCGCACTTAACGCCAGCCACTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAGCGGCGAATCAAATAGCCGGATATAA > minE/754096‑754230
|
tCAGCGCACTTAACGCCAGCCACTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATcc < 1:1125134/69‑1 (MQ=255)
tCAGCGCACTTAACGCCAGCCACTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATcc < 1:2045163/69‑1 (MQ=255)
tCAGCGCACTTAACGCCAGCCACTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATcc < 1:2682250/69‑1 (MQ=255)
aaCGCCAGCCACTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCgag > 1:1287151/1‑68 (MQ=255)
aaCGCCAGCCACTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCgag > 1:2597278/1‑68 (MQ=255)
ccagccaCTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAAt < 1:2144805/69‑1 (MQ=255)
ccagccaCTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAAt < 1:2374142/69‑1 (MQ=255)
ccagccaCTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAAt < 1:2576802/69‑1 (MQ=255)
ccagccaCTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAAt < 1:2580680/69‑1 (MQ=255)
ccagccaCTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAAt < 1:157443/69‑1 (MQ=255)
ccagccaCTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAAt < 1:1735071/69‑1 (MQ=255)
cagccaCTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAAt < 1:1069080/68‑1 (MQ=255)
cagccaCTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAAt < 1:2075645/68‑1 (MQ=255)
gCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCAc > 1:2737610/1‑68 (MQ=255)
ccAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTTCGCTGTc > 1:1453149/1‑69 (MQ=255)
ccAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTc > 1:1065887/1‑69 (MQ=255)
ccAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTc > 1:2505643/1‑69 (MQ=255)
ccAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTc > 1:848479/1‑69 (MQ=255)
ccAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTc > 1:1101633/1‑69 (MQ=255)
ccAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTc > 1:2216700/1‑69 (MQ=255)
aaaGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa < 1:572717/69‑1 (MQ=255)
aaaGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa < 1:2553403/69‑1 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCg > 1:753686/1‑67 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:2247609/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:930894/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:721386/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:622580/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:3254408/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:325293/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:324478/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:3212336/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:314026/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:3109241/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:307543/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:3046074/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:2074105/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:2054542/1‑68 (MQ=255)
aaGCGCCAGCACCCAGAAGATGTTCCAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGa > 1:1557652/1‑68 (MQ=255)
gcgcCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGatat < 1:253915/69‑1 (MQ=255)
cAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAgcg < 1:470845/69‑1 (MQ=255)
aGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAgcg < 1:710411/68‑1 (MQ=255)
aGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAgcg < 1:197323/68‑1 (MQ=255)
gaTGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAgcg < 1:2906962/57‑1 (MQ=255)
ccAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAgc < 1:432102/50‑1 (MQ=255)
ccAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAgc < 1:217195/50‑1 (MQ=255)
ccAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAgc < 1:804298/50‑1 (MQ=255)
ccAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAgc < 1:7708/50‑1 (MQ=255)
ccAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAgc < 1:2286458/50‑1 (MQ=255)
ccAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAgc < 1:2037112/50‑1 (MQ=255)
ccAGATGCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAgc < 1:1554713/50‑1 (MQ=255)
ccAGATGCGTTTATCGAGA‑AATTTCCCCACGGTACGCTGTCGATATAgc < 1:1507877/49‑1 (MQ=38)
ccAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAGCGGCGAATCAAATAGCCGGa > 1:62679/1‑69 (MQ=255)
ccAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAGCGGCGAATCAAATAGCCGGa > 1:2346787/1‑69 (MQ=255)
ccAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAGCGGCGAATCAAATAGCCGGa > 1:2635083/1‑69 (MQ=255)
ccAGATCCGTTTATCGAGACAATTTCCCAACGGTACGCTGTCGATATAGAGGCGAATCAAATAGCCGGa > 1:3116256/1‑69 (MQ=255)
ccGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAGCGGCGAATCAAATAGCCGGATATaa > 1:240217/1‑68 (MQ=255)
ccGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAGCGGCGAATCAAATAGCCGGATATaa > 1:636332/1‑68 (MQ=255)
ccGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAGCGGCGAATCAAATAGCCGGATATaa > 1:1958039/1‑68 (MQ=255)
ccGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAGCGGCGAATCAAATAGCCGGATATaa > 1:1782610/1‑68 (MQ=255)
ccGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAGCGGCGAATCAAATAGCCGGATATaa > 1:1421971/1‑68 (MQ=255)
|
TCAGCGCACTTAACGCCAGCCACTGCACCACGCCCCAAAGCGCCAGCACCCAGAAGATGTTCCAGATCCGTTTATCGAGACAATTTCCCCACGGTACGCTGTCGATATAGCGGCGAATCAAATAGCCGGATATAA > minE/754096‑754230
|
| 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
