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 |
|
A1 F28 I2 R2
|
356 |
55.1 |
4139924 |
95.4% |
3949487 |
63.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,272,678 |
A→T |
S245S (TCT→TCA) |
garL ← |
alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,272,678 | 0 | A | T | 80.4%
| 115.2
/ 24.2
| 51 | S245S (TCT→TCA) | garL | alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase |
| Reads supporting (aligned to +/- strand): ref base A (1/9); new base T (27/14); total (28/23) |
| Fisher's exact test for biased strand distribution p-value = 2.91e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01 |
TCAATCATCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCAGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAACGACGC > W3110S.gb/3272614‑3272744
|
tcaatcaTCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCGAGTTTCTGAGTGGCa < 1:319928/65‑1 (MQ=255)
tcaatcaTCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCa < 1:4130610/65‑1 (MQ=255)
tcaatcaTCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCa < 1:372860/65‑1 (MQ=255)
tcaatcaTCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCa < 1:2285462/65‑1 (MQ=255)
tcaatcaTCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCa < 1:2207372/65‑1 (MQ=255)
tcaatcaTCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCg > 1:3647787/1‑70 (MQ=255)
tcaatcaTCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCg > 1:3717049/1‑70 (MQ=255)
tcaatcaTCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCg > 1:2810942/1‑70 (MQ=255)
tcaatcaTCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCg > 1:2406224/1‑70 (MQ=255)
tcaatcaTCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCg > 1:3568491/1‑70 (MQ=255)
tcaatcaTCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCg > 1:4098283/1‑70 (MQ=255)
tcatcTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGa < 1:3057071/71‑1 (MQ=255)
tcatcTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGa < 1:1762401/71‑1 (MQ=255)
tcatcTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGa < 1:1799613/71‑1 (MQ=255)
tcatcTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGa < 1:2018771/71‑1 (MQ=255)
tcatcTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGa < 1:2804488/71‑1 (MQ=255)
tcatcTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGa < 1:153139/71‑1 (MQ=255)
tcatcTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGa < 1:2631689/71‑1 (MQ=255)
tcatcTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGa < 1:2596106/71‑1 (MQ=255)
tcatcTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGAAAGa < 1:1802477/71‑1 (MQ=255)
ctctctTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGcc > 1:3677649/1‑71 (MQ=255)
ctctctTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGcc > 1:2912756/1‑71 (MQ=255)
ctctctTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGcc > 1:3408303/1‑71 (MQ=255)
ctctctTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGcc > 1:3261448/1‑71 (MQ=255)
tctctTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCgg < 1:1520918/62‑1 (MQ=255)
tctctTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCgg < 1:2029769/62‑1 (MQ=255)
tctTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCAGAGCGGaa < 1:2562996/62‑1 (MQ=255)
tctTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCAGAGCGGaa < 1:136605/62‑1 (MQ=255)
tctTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCAGAGCGGaa < 1:2803934/62‑1 (MQ=255)
ttgttgCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGCCgag < 1:162113/69‑1 (MQ=255)
ttgttgCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGCCgag < 1:3921659/69‑1 (MQ=255)
ttgttgCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCAGAGCGGAAGa > 1:2442771/1‑62 (MQ=255)
tggtTATTTTTTAAAGGTATCAGCCAGTTTCT‑AGTGGCTGAGCGGAAGa < 1:1423239/49‑1 (MQ=38)
tATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCgg > 1:3266903/1‑42 (MQ=255)
tATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGCCGAGAt > 1:3396619/1‑55 (MQ=255)
tATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGCCGAGAt > 1:2338139/1‑55 (MQ=255)
tATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGCCGAGAt > 1:2703883/1‑55 (MQ=255)
tATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGCCGAGAt > 1:2255646/1‑55 (MQ=255)
tATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGCCGAGAt > 1:1262514/1‑55 (MQ=255)
tATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGCCGAGAt > 1:764196/1‑55 (MQ=255)
tATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGccc > 1:2164486/1‑71 (MQ=255)
tATCAGCCAGTTTCTGAGTGGCTGAGCGGAAGACGCCGAGATCGCTGCCGACAGACACAAACGt > 1:822857/1‑64 (MQ=255)
aGTGGCTGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAacgac > 1:834164/1‑71 (MQ=255)
aGTGGCTGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAacgac > 1:3766813/1‑71 (MQ=255)
aGTGGCAGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAac < 1:2965337/68‑1 (MQ=255)
aGTGGCAGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAac < 1:2313634/68‑1 (MQ=255)
aGTGGCAGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAac < 1:1580435/68‑1 (MQ=255)
aGTGGCAGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAac < 1:1215682/68‑1 (MQ=255)
aGTGGCAGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAac < 1:121505/68‑1 (MQ=255)
aGTGGCAGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAac < 1:1006016/68‑1 (MQ=255)
tGGCTGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAacgacg > 1:2599461/1‑70 (MQ=255)
tGGCTGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAacgacg > 1:4098592/1‑70 (MQ=255)
tGGCTGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAACGAcgc > 1:320285/1‑71 (MQ=255)
tGGCTGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAACGAcgc > 1:3783603/1‑71 (MQ=255)
tGGCTGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAACGAcgc > 1:1617272/1‑71 (MQ=255)
tGGCTGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAACGAcgc > 1:1268692/1‑71 (MQ=255)
|
TCAATCATCTCTCTTGTTGCGGTGGTGGTTATTTTTTAAAGGTATCAGCCAGTTTCTGAGTGGCAGAGCGGAAGACGCCGAGATCGCTGCCGACAGCCACAAACGTCGCGCCCCATTCCAGATAACGACGC > W3110S.gb/3272614‑3272744
|
| 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
