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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,079,041 |
A→G |
100% |
I417I (ATT→ATC) |
tktA ← |
transketolase 1, thiamin‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,079,041 | 0 | A | G | 96.6%
| 195.1
/ ‑1.8
| 58 | I417I (ATT→ATC) | tktA | transketolase 1, thiamin‑binding |
| Reads supporting (aligned to +/- strand): ref base A (2/0); new base G (26/30); total (28/30) |
| Fisher's exact test for biased strand distribution p-value = 2.29e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTG > W3110S.gb/3078973‑3079108
|
tATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGAt > 1:3158495/1‑71 (MQ=255)
tATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGAt > 1:3693848/1‑71 (MQ=255)
tATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGAt > 1:389074/1‑71 (MQ=255)
tATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGAt > 1:422485/1‑71 (MQ=255)
tATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGAt > 1:591831/1‑71 (MQ=255)
tATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGAt > 1:2924069/1‑71 (MQ=255)
ttCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATcg > 1:1473722/1‑71 (MQ=255)
ttCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATcg > 1:2345086/1‑71 (MQ=255)
ccACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATcgcg > 1:2812781/1‑71 (MQ=255)
ccACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATcgcg > 1:2753511/1‑71 (MQ=255)
ccACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATcgcg > 1:1405225/1‑71 (MQ=255)
ccACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATcgcg > 1:2749095/1‑71 (MQ=255)
cACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATcgcg < 1:3400353/70‑1 (MQ=255)
cACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATcgcg < 1:707399/70‑1 (MQ=255)
cACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATcgcg < 1:2182385/70‑1 (MQ=255)
cACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATcgcg < 1:1806593/70‑1 (MQ=255)
aCGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGt < 1:1992998/71‑1 (MQ=255)
cGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGt > 1:1672724/1‑70 (MQ=255)
cGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGt > 1:3616711/1‑70 (MQ=255)
cGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGt > 1:2609389/1‑70 (MQ=255)
aCATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATa > 1:835293/1‑71 (MQ=255)
aCATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATa > 1:1932108/1‑71 (MQ=255)
aCATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATa > 1:1262297/1‑71 (MQ=255)
gTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTcgcg < 1:1584938/71‑1 (MQ=255)
tGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTcgcg < 1:1392253/70‑1 (MQ=255)
gAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAac < 1:1897295/71‑1 (MQ=255)
gAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAac < 1:3484557/71‑1 (MQ=255)
gAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAac < 1:808063/71‑1 (MQ=255)
gtgtACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACAcc > 1:2543045/1‑71 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTcgcg < 1:3467481/62‑1 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTcgcg < 1:3261586/62‑1 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTcgcg < 1:2938679/62‑1 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTcgcg < 1:499135/62‑1 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTcgcg < 1:1643401/62‑1 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGt < 1:3310765/70‑1 (MQ=255)
tACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGt < 1:953875/70‑1 (MQ=255)
gCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGaa > 1:1116166/1‑60 (MQ=255)
gCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGaa > 1:3369652/1‑60 (MQ=255)
gCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGaa > 1:1225032/1‑60 (MQ=255)
gCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGaa > 1:2710011/1‑60 (MQ=255)
gCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTg > 1:1152556/1‑70 (MQ=255)
gAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTcgcg < 1:3254859/54‑1 (MQ=255)
gAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTcgcg < 1:2985961/54‑1 (MQ=255)
gAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTcgcg < 1:2465757/54‑1 (MQ=255)
gAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGt < 1:1113135/71‑1 (MQ=255)
gAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGt < 1:1236844/71‑1 (MQ=255)
gAAGCCACCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGt < 1:326195/71‑1 (MQ=255)
aCCGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTAc > 1:3168378/1‑71 (MQ=255)
cGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTg < 1:1476309/58‑1 (MQ=255)
cGTGCAGGGAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTg < 1:2913989/58‑1 (MQ=255)
ggAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCgcagca < 1:1706311/70‑1 (MQ=255)
ggAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCgcagca < 1:2370314/70‑1 (MQ=255)
ggAGATACCGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCgcagca < 1:1227943/70‑1 (MQ=255)
ccGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGtt < 1:570423/71‑1 (MQ=255)
ccGTTAGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGtt < 1:2892700/71‑1 (MQ=255)
ccGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGtt > 1:2086125/1‑71 (MQ=255)
ccGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGtt > 1:808102/1‑71 (MQ=255)
aGCGATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTg > 1:672235/1‑71 (MQ=255)
|
TATTCCACGAACATCAGGAAGGTGGAGGTGTACGGCAGGAAGCCACCGTGCAGGGAGATACCGTTAGCAATCGCGGTCATACCGAACTCGCGAACACCGTAGTGGATGTAGTTACCCGCAGCATCTTCGTTGATTG > W3110S.gb/3078973‑3079108
|
| 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
