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 |
365,751 |
G→C |
28.3% |
V547V (GTC→GTG) |
fepA ← |
iron‑enterobactin outer membrane transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 365,751 | 0 | G | C | 28.3%
| 78.3
/ 35.1
| 60 | V547V (GTC→GTG) | fepA | iron‑enterobactin outer membrane transporter |
| Reads supporting (aligned to +/- strand): ref base G (22/21); new base C (6/11); total (28/32) |
| Fisher's exact test for biased strand distribution p-value = 3.90e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.22e-01 |
TGCGTTTTGCCCTACAGCCACATAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTTTGTT > minE/365685‑365801
|
tGCGTTTTGCCCTACAGCCACATAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGAc > 1:3270949/1‑69 (MQ=255)
cAGCCACATAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCcccc > 1:3126556/1‑69 (MQ=255)
cAGCCACATAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCAcc > 1:2283130/1‑69 (MQ=255)
cAGCCACATAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCAcc > 1:2493196/1‑69 (MQ=255)
gCCACATAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCg > 1:2915335/1‑69 (MQ=255)
cacaTAGCCCGCTTCTATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTc > 1:1533982/1‑69 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTc > 1:2741633/1‑69 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTc > 1:13988/1‑69 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTCACGCCCGCCAGCCAACCGTc < 1:200213/69‑1 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTCACGCCCGCCAGCCAACCGTc < 1:2939301/69‑1 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTCACGCCCGCCAGCCAACCGTc < 1:158100/69‑1 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTCACGCCCGCCAGCCAACCGTc < 1:3282905/69‑1 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTCACGCCCGCCAGCCAACCGTc < 1:3304412/69‑1 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTCACGCCCGCCAGCCAACCGTc < 1:3345597/69‑1 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTCACGCCCGCCAGCCAACCGTc < 1:3349459/69‑1 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTCACGCCCGCCAGCCAACCGTc < 1:399799/69‑1 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTCACGCCCGCCAGCCAACCGTc < 1:485492/69‑1 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTCACGCCCGCCAGCCAACCGTc < 1:1050299/69‑1 (MQ=255)
cacaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGAGACGCCCGCCAGCCACCCCTc > 1:2739056/1‑69 (MQ=255)
acaTAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTCACGCCCGCCAGCCAACCGTc < 1:1652038/68‑1 (MQ=255)
tAGCCCGCTTCGATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGt > 1:2521273/1‑69 (MQ=255)
tAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTcgcg > 1:2745331/1‑68 (MQ=255)
tAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGt > 1:842885/1‑69 (MQ=255)
tAGCCCGCTTCAATCTTATTGCGATAATCGTTAAGGAACCAGGTGACGCCCGCCGGCCACCCGTcgcg > 1:1751474/1‑68 (MQ=255)
tAGCCCGCATCAATCTTATTGCGATAATCGTTACGGAAGCAGGTGAc > 1:2318634/1‑47 (MQ=255)
ccGCTTCAATCTTATTGCGATAATCGTTACTGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTg < 1:2220963/68‑1 (MQ=255)
ccGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTg < 1:612359/68‑1 (MQ=255)
ccGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTg < 1:2640827/68‑1 (MQ=255)
ccGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTg < 1:1152778/68‑1 (MQ=255)
ttCAATCTTATTGGGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTc < 1:1221550/69‑1 (MQ=255)
ttCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTc < 1:2303197/69‑1 (MQ=255)
ttCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTc < 1:373550/69‑1 (MQ=255)
ttCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTc < 1:3271339/69‑1 (MQ=255)
ttCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTc < 1:1910877/69‑1 (MQ=255)
ttCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTc < 1:325821/69‑1 (MQ=255)
ttCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTc < 1:2705978/69‑1 (MQ=255)
tCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTc < 1:1676248/68‑1 (MQ=255)
aaTCTTATTGCGATAATCGTTACGGCACCAGGTCAcgcccgc > 1:2957554/1‑42 (MQ=38)
aaTCTTATTGCGATAATCGTTACGGAACCAGGTCAcgcccgc > 1:1994228/1‑42 (MQ=255)
aaTCTTATTGCGATAATCGTTACGGAACCAGGTCAcgcccgc > 1:388663/1‑42 (MQ=255)
aaTCTTATTGCGATAATCGTTACGGAACCAGGTCAcgcccgc > 1:187827/1‑42 (MQ=255)
aaTCTTATTGCGATAATCGTTACGGAACCAGGTCAcgcccgc > 1:2707086/1‑42 (MQ=255)
aaTCTTATTGCGATAATCGTTACGGAACCAGGTCAcgc > 1:1692232/1‑38 (MQ=255)
aTTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTg > 1:2009024/1‑55 (MQ=255)
aTTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTg > 1:2426930/1‑55 (MQ=255)
aTTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCaa > 1:1077074/1‑68 (MQ=255)
aTTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCaa > 1:2462815/1‑68 (MQ=255)
aTTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCaa > 1:2780260/1‑68 (MQ=255)
gCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTcgct < 1:480618/48‑2 (MQ=255)
gCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTcgcg < 1:2954902/48‑1 (MQ=255)
gCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTcgcg < 1:2641692/48‑1 (MQ=255)
gCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTcgcg < 1:194159/48‑1 (MQ=255)
gCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTcgcg < 1:1282123/48‑1 (MQ=255)
gATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTc < 1:1429531/55‑1 (MQ=255)
aTCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGATCAATCTCTttgtt < 1:1346338/69‑1 (MQ=255)
aTCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCaa > 1:2559137/1‑59 (MQ=255)
aTCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAAt > 1:1072300/1‑60 (MQ=255)
aTCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAAt > 1:237861/1‑60 (MQ=255)
aTCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt < 1:1304709/69‑1 (MQ=255)
tCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt < 1:536229/68‑1 (MQ=255)
gACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCaa > 1:1615818/1‑41 (MQ=255)
gACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt > 1:145905/1‑51 (MQ=255)
gACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt < 1:29644/51‑1 (MQ=255)
gACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt < 1:52527/51‑1 (MQ=255)
gACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt > 1:2626558/1‑51 (MQ=255)
|
TGCGTTTTGCCCTACAGCCACATAGCCCGCTTCAATCTTATTGCGATAATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTTTGTT > minE/365685‑365801
|
| 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
