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 |
1,967,112 |
A→G |
48.1% |
G506G (GGT→GGC) |
tktA ← |
transketolase 1, thiamin‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,967,112 | 0 | A | G | 48.1%
| ‑3.5
/ 44.9
| 52 | G506G (GGT→GGC) | tktA | transketolase 1, thiamin‑binding |
| Reads supporting (aligned to +/- strand): ref base A (11/16); new base G (8/17); total (19/33) |
| Fisher's exact test for biased strand distribution p-value = 5.74e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGT > minE/1967045‑1967177
|
ttcgttcCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAacac < 1:872078/69‑1 (MQ=255)
cgttcCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGCCGCTCAACACCg > 1:1713725/1‑69 (MQ=255)
cgttcCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCg > 1:2827431/1‑69 (MQ=255)
cgttcCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCg > 1:2296874/1‑69 (MQ=255)
cgttcCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCg > 1:2249607/1‑69 (MQ=255)
cgttcCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCg > 1:671451/1‑69 (MQ=255)
cgttcCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCg > 1:445993/1‑69 (MQ=255)
cgttcCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCg > 1:1864108/1‑69 (MQ=255)
ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCTTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:1168562/68‑1 (MQ=255)
ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:1816989/68‑1 (MQ=255)
ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:3121681/68‑1 (MQ=255)
ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:3153931/68‑1 (MQ=255)
ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:2129643/68‑1 (MQ=255)
ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:333217/68‑1 (MQ=255)
ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:390970/68‑1 (MQ=255)
ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:1813800/68‑1 (MQ=255)
ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:395459/68‑1 (MQ=255)
ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:1459535/68‑1 (MQ=255)
ccAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:1302308/68‑1 (MQ=255)
ccAGGTTCTGACGGGAGAGGAGCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:1610706/68‑1 (MQ=255)
gATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:867034/49‑1 (MQ=255)
tGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACg < 1:125759/68‑1 (MQ=255)
gCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCAcgcg < 1:2161110/42‑1 (MQ=255)
gTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGc < 1:3253154/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTTGTCACACGGACGCCATGTAGACATGTTCggg < 1:1402776/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:2459884/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:369489/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:72749/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:328527/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:3183661/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:2943917/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:1133656/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:2797177/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:100618/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:2450057/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:1355442/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:13890/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:1615258/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:1464835/69‑1 (MQ=255)
tCAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGGCACACGGACGCCATGTAGACATGTTCggg < 1:1980384/69‑1 (MQ=255)
cAACGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg < 1:1453415/68‑1 (MQ=255)
cAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg > 1:3068782/1‑68 (MQ=255)
cAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg > 1:2326213/1‑68 (MQ=255)
cAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg > 1:697245/1‑68 (MQ=255)
cAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCggg > 1:51638/1‑68 (MQ=255)
aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTcac > 1:824840/1‑41 (MQ=37)
aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt > 1:1898502/1‑69 (MQ=255)
aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt > 1:595338/1‑69 (MQ=255)
aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt > 1:522313/1‑69 (MQ=255)
aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt > 1:287647/1‑69 (MQ=255)
aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt > 1:1956869/1‑69 (MQ=255)
aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt > 1:3232132/1‑69 (MQ=255)
aaCGCCGTATTTCCACGCTACTGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGt > 1:2963549/1‑69 (MQ=255)
acCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACg < 1:2433625/41‑1 (MQ=255)
|
TTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACCGCGGATTCAACCTGGTCACACGGACGCCATGTAGACATGTTCGGGGT > minE/1967045‑1967177
|
| 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
