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 |
1,920,438 |
G→A |
31.4% |
A154A (GCC→GCT) |
ygeD ← |
predicted inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,920,438 | 0 | G | A | 31.4%
| 66.5
/ 33.8
| 73 | A154A (GCC→GCT) | ygeD | predicted inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base G (24/26); new base A (4/19); total (28/45) |
| Fisher's exact test for biased strand distribution p-value = 1.88e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.35e-01 |
ACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTT > minE/1920375‑1920506
|
accGTAGGCCAGTGCGCATGCGGCCAGGGCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTa > 1:3017972/1‑68 (MQ=255)
accGTAGGCCAGTGCGCATGCGGCCAGGGCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTa > 1:1055469/1‑68 (MQ=255)
accGTAGGCCAGTGCGCATGCGGCCAGGGCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTa > 1:2559912/1‑68 (MQ=255)
accGTAGGCCAGTGCGCATGCGGCCAGGGCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTa > 1:1182093/1‑68 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa > 1:1937302/1‑69 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa > 1:2356292/1‑69 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa > 1:2330254/1‑69 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa > 1:499807/1‑69 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa > 1:1900454/1‑69 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa > 1:1850487/1‑69 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa > 1:75424/1‑69 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa > 1:1180425/1‑69 (MQ=255)
tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa > 1:1286423/1‑69 (MQ=255)
cgcATGCGGCCAGGGCGCCGAGGAAATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaaaa > 1:1479506/1‑69 (MQ=255)
cgcATGCGGCCAGGGCGACGAGGAAATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaaaa > 1:1483272/1‑69 (MQ=255)
cGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGa < 1:251683/52‑1 (MQ=255)
cGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgcc > 1:1457340/1‑68 (MQ=255)
cGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgcc > 1:2510034/1‑68 (MQ=255)
cGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgcc > 1:724788/1‑68 (MQ=255)
cGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgcc > 1:1815907/1‑68 (MQ=255)
gCCAGGGCTACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCt < 1:1088963/69‑1 (MQ=255)
gCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgccgc < 1:1612537/68‑1 (MQ=255)
gCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgccgc < 1:2169492/68‑1 (MQ=255)
gCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCt < 1:3007670/69‑1 (MQ=255)
gCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCt < 1:500842/69‑1 (MQ=255)
gCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCt < 1:1161667/69‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:1612658/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:775523/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:3038177/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:3219201/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:28394/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:2821113/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:2752026/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:3294457/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:805889/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:2467480/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:728535/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:2283442/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:1608864/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:618782/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:77658/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:1200869/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:1966193/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:506493/63‑1 (MQ=255)
gggCAACCAGAATATGCCAGGCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg < 1:2716555/63‑1 (MQ=255)
acgaGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGaa < 1:2396357/69‑1 (MQ=255)
acgaGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGaa < 1:2147071/69‑1 (MQ=255)
gACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTc < 1:1617154/69‑1 (MQ=255)
gACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTc < 1:2690746/69‑1 (MQ=255)
gACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTc < 1:2641181/69‑1 (MQ=255)
gACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTc < 1:2544185/69‑1 (MQ=255)
gACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTc < 1:1595725/69‑1 (MQ=255)
gACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTc < 1:1602514/69‑1 (MQ=255)
gACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTc < 1:3398338/69‑1 (MQ=255)
aCATGCCAGTCAGCCAGCACACCACCGGCTACGAAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTc < 1:97343/68‑1 (MQ=255)
ccAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCt > 1:157762/1‑49 (MQ=255)
ccAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTa > 1:1142935/1‑50 (MQ=255)
ccAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTAt > 1:2925361/1‑51 (MQ=255)
ccAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTAt > 1:840263/1‑51 (MQ=255)
ccAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTAt > 1:1238103/1‑51 (MQ=255)
ccAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTAt > 1:1605094/1‑51 (MQ=255)
ccAGTCAGCCAGCACACCACCGGCTACGGAACAGAGCAAAATCGCCGCTAt > 1:2188868/1‑51 (MQ=255)
cagccagcACACCACCGGCTACGGAACCGAGCAAAATcgccgc < 1:2188270/43‑1 (MQ=255)
cagccagcACACCACCGGCTACGGAACCGAGCAAAATcgccgc < 1:520011/43‑1 (MQ=255)
cagccagcACACCACCGGCTACGGAACCGAGCAAAATcgccgc < 1:1889120/43‑1 (MQ=255)
cagccagcACACCACCGGCTACGGAACCGAGCAAAATcgccgc < 1:68454/43‑1 (MQ=255)
cagccagcACACCACCGGCTACGGAACCGAGCAAAATcgccgc < 1:1866859/43‑1 (MQ=255)
cagccagcACACCACCGGCTACGGAACCGAGCAAAATcgccgc < 1:2368766/43‑1 (MQ=255)
cagccagcACACCACCGGCTACGGAACCGAGCAAAATcgccgc < 1:1568162/43‑1 (MQ=255)
cagccagcACACCACCGGCTACGGAACCGAGCAAAATcgccgc < 1:1149006/43‑1 (MQ=255)
cagccagcACACCACCGGCTACGGAACCGAGCAAAATcgccgc < 1:2850871/43‑1 (MQ=255)
cagccagcACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAAcc > 1:2244264/1‑67 (MQ=255)
agccagcACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTc > 1:3033605/1‑57 (MQ=255)
ggCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACtt < 1:2653235/69‑1 (MQ=255)
|
ACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAAGCTTCCATTAAACCGTTAGCTTTCACTAACTT > minE/1920375‑1920506
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
