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 |
2,616,163 |
C→T |
37.0% |
V236V (GTC→GTT) |
yhhS → |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,616,163 | 0 | C | T | 37.0%
| 36.6
/ 36.2
| 62 | V236V (GTC→GTT) | yhhS | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base C (28/11); new base T (9/14); total (37/25) |
| Fisher's exact test for biased strand distribution p-value = 1.62e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
GTGCTTGGGCGCGTCTGGCTGTACGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTC > minE/2616101‑2616220
|
gTGCTTGGGCGCGTCTGGCTGTACGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGcc < 1:968954/69‑1 (MQ=255)
gTGCTTGGGCGCGTCTGGCTGTACGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGcc < 1:482892/69‑1 (MQ=255)
gTGCTTGGGCGCGTCTGGCTGTACGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGcc < 1:3399756/69‑1 (MQ=255)
gTGCTTGGGCGCGTCTGGCTGTACGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGcc < 1:3221591/69‑1 (MQ=255)
gTGCTTGGGCGCGTCTGGCTGTACGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGcc < 1:2648834/69‑1 (MQ=255)
gTGCTTGGGCGCGTCTGGCTGTACGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGcc < 1:143806/69‑1 (MQ=255)
cgcgTCTGGCTGTACGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCGTCGCCACCTTTAt < 1:2502305/68‑1 (MQ=255)
cgcgTCTGGCTGTACGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTAt < 1:381517/68‑1 (MQ=255)
cGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATg > 1:3373616/1‑68 (MQ=255)
cGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGa > 1:749166/1‑69 (MQ=255)
cGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGa < 1:473214/69‑1 (MQ=255)
cGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGa > 1:2498317/1‑69 (MQ=255)
cGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGa > 1:361145/1‑69 (MQ=255)
cGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGa > 1:18072/1‑69 (MQ=255)
cGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGa > 1:2629840/1‑69 (MQ=255)
gcgcTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTaa < 1:2305823/68‑1 (MQ=255)
gcgcTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTaa > 1:2403638/1‑68 (MQ=255)
gcgcTGGCACTGGCTTCCGACGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTaa < 1:2362430/68‑1 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGGCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:3281179/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAgg > 1:1581339/1‑60 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:3181242/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:2946465/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:2688802/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:2452770/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:460276/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:487236/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:1300969/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:1452416/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:2201522/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:2195152/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:1270388/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACgg > 1:1961441/1‑69 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACg > 1:117991/1‑68 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACg > 1:1933588/1‑68 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACg > 1:286372/1‑68 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACg > 1:3134655/1‑68 (MQ=255)
ggCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGATGTTTTATGACGCTAAAGGTTGGGACgg > 1:743688/1‑69 (MQ=255)
gCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGt > 1:1795963/1‑69 (MQ=255)
gCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGt > 1:1993656/1‑69 (MQ=255)
ccgGATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCtt > 1:1310633/1‑69 (MQ=255)
ccgGATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCtt > 1:71665/1‑69 (MQ=255)
ccgGATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCtt > 1:112810/1‑69 (MQ=255)
ccgGATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCtt > 1:1936280/1‑69 (MQ=255)
ccgGATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCtt > 1:74550/1‑69 (MQ=255)
ccgGATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCtt > 1:2732315/1‑69 (MQ=255)
ccgGATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCtt > 1:1005195/1‑69 (MQ=255)
ccgGATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCtt > 1:861409/1‑69 (MQ=255)
ccgGATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCt > 1:1238559/1‑68 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:879038/69‑1 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:899213/69‑1 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:630591/69‑1 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:1057241/69‑1 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:1107984/69‑1 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:1495939/69‑1 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:3250435/69‑1 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:1164602/69‑1 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:2750703/69‑1 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:2220650/69‑1 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:226507/69‑1 (MQ=255)
ggATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:2442934/69‑1 (MQ=255)
gATTTGGCGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:467656/68‑1 (MQ=255)
cGTTATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTc < 1:2303485/61‑1 (MQ=255)
|
GTGCTTGGGCGCGTCTGGCTGTACGGTATGGCGCTGGCACTGGCTTCCGCCGGATTTGGCGTCATCGCCACCTTTATCACGCTGTTTTATGACGCTAAAGGTTGGGACGGTGCGGCTTTC > minE/2616101‑2616220
|
| 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
