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 F1 I0 R2
|
532 |
47.8 |
3863072 |
94.9% |
3666055 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,452,626 |
A→C |
25.5% |
D937E (GAT→GAG) |
rpoB ← |
RNA polymerase, beta subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,452,626 | 0 | A | C | 25.5%
| 62.0
/ 43.5
| 60 | D937E (GAT→GAG) | rpoB | RNA polymerase, beta subunit |
| Reads supporting (aligned to +/- strand): ref base A (21/23); new base C (8/7); total (29/31) |
| Fisher's exact test for biased strand distribution p-value = 7.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01 |
CTTCGCCTGTTTGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCAGAGAAGA > W3110S.gb/3452566‑3452691
|
cttcGCCTGTTTGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTa < 1:3237544/70‑1 (MQ=255)
cGCCTGTTTGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTaa < 1:3600717/68‑1 (MQ=255)
cGCCTGTTTGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTaa < 1:2494317/68‑1 (MQ=255)
tttGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATcgc < 1:3235395/56‑1 (MQ=255)
tttGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATcgc < 1:538909/56‑1 (MQ=255)
tttGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGaa > 1:482939/1‑71 (MQ=255)
tGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGaa > 1:3288689/1‑69 (MQ=255)
tGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGaa > 1:1319389/1‑69 (MQ=255)
tGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACg > 1:3280061/1‑71 (MQ=255)
tGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACg > 1:2418783/1‑71 (MQ=255)
aGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTc < 1:1079724/71‑1 (MQ=255)
tGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGCCCTGAACGTCGa > 1:1455295/1‑70 (MQ=255)
aTTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAAc < 1:228782/71‑1 (MQ=255)
aTTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTATACGCCATCGCGAGTAAAGACCTGAACGTCGATAAc < 1:2197562/71‑1 (MQ=255)
tttCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAAcc > 1:3165029/1‑71 (MQ=255)
tcttcGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGa > 1:3843361/1‑64 (MQ=255)
tcttcGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGAt > 1:86148/1‑65 (MQ=255)
cttcGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTa > 1:2375164/1‑71 (MQ=255)
cttcGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTa > 1:1147487/1‑71 (MQ=255)
ttcGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGt < 1:1214315/69‑1 (MQ=255)
cGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCg > 1:1152618/1‑71 (MQ=255)
gATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCg < 1:1337687/70‑1 (MQ=255)
tCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATa > 1:600337/1‑70 (MQ=255)
gcgcACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCg < 1:946726/71‑1 (MQ=255)
gcACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGtt < 1:2867510/71‑1 (MQ=255)
tcttcgtCTTTTTCTACACCCTCGtttagttgcttctttt < 1:2205785‑M2/38‑17 (MQ=255)
tcttcgtCTTTTTCTACACCCTCGtttagttgcttctttt < 1:2962878‑M2/38‑17 (MQ=255)
gTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTgg < 1:3086973/70‑1 (MQ=255)
ttcGTCTTTTTCTACGCCCTCGtttagttgcttcttt > 1:1918110‑M2/1‑22 (MQ=255)
ttcGTCTTTTTCTACACCCTCGtttagttgcttctttttccttcccgctt > 1:3129305‑M2/1‑22 (MQ=255)
cgtCTTTTTCTACGCCCTCGtttagttgcttctttttccttcccgct < 1:2880706‑M2/46‑28 (MQ=255)
cgtCTTTTTCTACGCCCTCGtttagttgcttctttttccttcc < 1:2965092‑M2/42‑24 (MQ=255)
cgtCTTTTTCTACACCCTCGtttagttgcttctttttcc < 1:1306607‑M2/38‑20 (MQ=255)
cgtCTTTTTCTACACCCTCGtttagttgcttctttt < 1:2108625‑M2/35‑17 (MQ=255)
cgtCTTTTTCTACACCCTCGtttagttgcttctttt < 1:69803‑M2/35‑17 (MQ=255)
gTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATaca < 1:3765510/58‑1 (MQ=255)
gTCTTTTTCTACACCCTCGtttagttgcttctttttccttcccgctt > 1:2640136‑M2/1‑19 (MQ=255)
gTCTTTTTCTACACCCTCGtttagttgcttctttttccttcccgctt > 1:2122780‑M2/1‑19 (MQ=255)
tttttCTACGCCCTCGtttagttgcttctttttcctt > 1:1261739‑M2/1‑16 (MQ=255)
tttttCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGa < 1:567601/51‑1 (MQ=255)
tttttCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGa < 1:2201268/51‑1 (MQ=255)
tttttCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTAcgcg > 1:1585854/1‑69 (MQ=255)
tttttCTACACCCTCGtttagttgcttctttttccttccc > 1:1389286‑M2/1‑16 (MQ=255)
tttttCTACACCCTCGtttagttgcttctttttcct > 1:2048913‑M2/1‑16 (MQ=255)
tttttCTACACCCTCGtttagttgcttctttttcct > 1:609077‑M2/1‑16 (MQ=255)
ttttCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTAcgcg > 1:2854008/1‑68 (MQ=255)
tttCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAAc > 1:2702545/1‑40 (MQ=255)
tttCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAAc > 1:2006435/1‑40 (MQ=255)
tttCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATa > 1:1125595/1‑51 (MQ=255)
tttCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCa > 1:325427/1‑69 (MQ=255)
ttCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCa > 1:3273889/1‑68 (MQ=255)
tCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCagag < 1:2728598/70‑1 (MQ=255)
tCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCagag < 1:2555328/70‑1 (MQ=255)
cTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCagag < 1:1503802/69‑1 (MQ=255)
cGCCGTCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCAGagaa < 1:1623377/68‑1 (MQ=255)
cGCCATCGCTAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCAGagaa < 1:291891/68‑1 (MQ=255)
cGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGtt < 1:2667838/52‑1 (MQ=255)
cGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCAGagaaga < 1:3509265/70‑1 (MQ=255)
cGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCAGagaag > 1:1759745/1‑69 (MQ=255)
cGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCAGagaa < 1:1210480/68‑1 (MQ=255)
|
CTTCGCCTGTTTGAGCTGCATTTCTTCGATTTCCAGCGCACGTTTGTCTTTTTCTACGCCATCGCGAGTAAAGACCTGAACGTCGATAACCGTACCGGATACACCGTTTGGTACGCGCAGAGAAGA > W3110S.gb/3452566‑3452691
|
| 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
