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 |
1,261,872 |
C→T |
48.5% |
S59S (TCG→TCA) |
torY ← |
TMAO reductase III (TorYZ), cytochrome c‑type subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,261,872 | 0 | C | T | 48.5%
| ‑2.5
/ 27.7
| 35 | S59S (TCG→TCA) | torY | TMAO reductase III (TorYZ), cytochrome c‑type subunit |
| Reads supporting (aligned to +/- strand): ref base C (7/11); new base T (3/14); total (10/25) |
| Fisher's exact test for biased strand distribution p-value = 2.64e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.06e-01 |
TCCCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCAA > minE/1261817‑1261935
|
tccCTGACTTTGGAATATGGCAATCTGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:3233063/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:1066898/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:1087820/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:758463/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:1258221/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:389285/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:3272367/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:1467106/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:3267129/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:3194867/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:1907099/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:2638125/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:2505744/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGaaaa < 1:2185875/61‑1 (MQ=255)
tccCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAg < 1:1067027/69‑1 (MQ=255)
tttGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGa < 1:2131264/69‑1 (MQ=255)
tttGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGa < 1:3108296/69‑1 (MQ=255)
tttGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGa < 1:1370891/69‑1 (MQ=255)
tttGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGa < 1:552005/69‑1 (MQ=255)
tttGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGa < 1:2421128/69‑1 (MQ=255)
tttGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGa < 1:820544/69‑1 (MQ=255)
tttGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGa < 1:2231342/69‑1 (MQ=255)
gCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGATATTCCTCaaa > 1:2328799/1‑69 (MQ=255)
gCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGATATTCCTCaaa > 1:445985/1‑69 (MQ=255)
gCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGATATTCCTCaaa > 1:2156267/1‑69 (MQ=255)
gCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGATATTCCTCaaa > 1:1602663/1‑69 (MQ=255)
gCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGATATTCCTCaaa > 1:310630/1‑69 (MQ=255)
gCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGATATTCCTCaa > 1:413721/1‑68 (MQ=255)
cAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGAAAAGTGGACAGTTCCCTGATATTCCTCaaaa > 1:74659/1‑69 (MQ=255)
cAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGAAAAGTGGACAGTTCCCTGATATTCCTCaaaa > 1:3037879/1‑69 (MQ=255)
cAATCGGCACATTCCGCACGTATCCCTTTCTGGTTTGAAAAGTGGACAGTTCCCTGATATTCCTCaaaa > 1:1675060/1‑69 (MQ=255)
cacaTTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTa < 1:2073317/68‑1 (MQ=255)
cacaTTCCGCACGTATCCCTTTCTGGTGCGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTa < 1:2144864/68‑1 (MQ=255)
ccGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCg < 1:1948354/69‑1 (MQ=255)
cTGGTTCGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGc > 1:2951307/1‑68 (MQ=255)
cGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGTCAGGAAAGGCaa < 1:2243452/64‑1 (MQ=255)
cGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCaa < 1:3059688/64‑1 (MQ=255)
cGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCaa < 1:1526042/64‑1 (MQ=255)
cGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCaa < 1:3399208/64‑1 (MQ=255)
cGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCaa < 1:1366804/64‑1 (MQ=255)
cGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCaa < 1:2767255/64‑1 (MQ=255)
cGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCaa < 1:26837/64‑1 (MQ=255)
cGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCaa < 1:736468/64‑1 (MQ=255)
cGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCaa < 1:2048351/64‑1 (MQ=255)
cGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCaa < 1:1136590/64‑1 (MQ=255)
cGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCaa < 1:868952/64‑1 (MQ=255)
|
TCCCTGACTTTGGAATATGGCAATCGGCACATTCCGCACGTATCCCTTTCTGGTTCGAAAAGTGGACAGTTCCCTGATATTCCTCAAAAGGTTTACTCATCGAGTGGCAGGAAAGGCAA > minE/1261817‑1261935
|
| 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
