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 |
2,912,172 |
T→G |
55.4% |
V42V (GTA→GTC) |
yjgF ← |
ketoacid‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,912,172 | 0 | T | G | 55.4%
| 20.0
/ 52.9
| 56 | V42V (GTA→GTC) | yjgF | ketoacid‑binding protein |
| Reads supporting (aligned to +/- strand): ref base T (8/17); new base G (15/16); total (23/33) |
| Fisher's exact test for biased strand distribution p-value = 2.78e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01 |
AGCGGCTTCGACGATCGCTTTTACGTTATCCAGCGACTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGTGATGATCATATTGCCCAGATCAA > minE/2912106‑2912236
|
aGCGGCTTCGACGATCGCTTTTACGTTATCCAGCGACTGACGTGCCTGTGCAGCGACGTCTGCCGGTAc > 1:2154885/1‑69 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:845221/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:2168361/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:2193522/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:1764430/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:1763148/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:1696682/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:3405521/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:2850770/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:3023834/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:921705/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:923136/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:1274088/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:957666/69‑1 (MQ=255)
tCGCTTTTACGTTATCCAGCGACTGACGCGCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:308749/69‑1 (MQ=255)
ttATCCAGCGACTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCggg < 1:2093153/69‑1 (MQ=255)
ttATCCAGCGACTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCggg < 1:2533052/69‑1 (MQ=255)
ttATCCAGCGACTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCggg < 1:2297705/69‑1 (MQ=255)
ttATCCAGCGACTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCggg < 1:22101/69‑1 (MQ=255)
ttATCCAGCGACTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCggg < 1:451206/69‑1 (MQ=255)
ttATCCAGCGACTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCggg < 1:2024928/69‑1 (MQ=255)
ttATCCAGCGACTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCggg < 1:1476298/69‑1 (MQ=255)
cTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGa < 1:2310052/69‑1 (MQ=255)
cTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGa < 1:3156767/69‑1 (MQ=255)
cTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGa < 1:906802/69‑1 (MQ=255)
cTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGa < 1:98050/69‑1 (MQ=255)
tGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGa < 1:3287850/68‑1 (MQ=255)
cgcgCCTGTGCATCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:307721/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:1130987/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:451211/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:523270/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:762678/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:884817/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:3355514/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:30197/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:1051782/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:1285626/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:1417978/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:1821308/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:2014460/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:2562529/4‑60 (MQ=255)
cgcgCCTGTGCAGCGACATCTGCCGGGACTTCGCCCGTTTTCGGGTTTACCGGGATCTGa > 1:3010111/4‑60 (MQ=255)
gTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGtg < 1:3362917/68‑1 (MQ=255)
gTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGtg < 1:1560799/68‑1 (MQ=255)
gTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGtg < 1:28578/68‑1 (MQ=255)
gtgCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGTGATGATCa < 1:774101/69‑1 (MQ=255)
gtgCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:863150/36‑1 (MQ=37)
gtgCAGCGACATCTGCCGGGACTTCGCCCGTTTTCg < 1:3120707/36‑1 (MQ=37)
cAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGTGATGATCat < 1:1395000/67‑1 (MQ=255)
ccGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCTGAGGTGATGATCATATTGCCCAGATCaa > 1:823768/1‑69 (MQ=255)
ccGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGTGATGATCATATTGCCCAGATCaa > 1:2126552/1‑69 (MQ=255)
ccGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGTGATGATCATATTGCCCAGATCaa > 1:1931109/1‑69 (MQ=255)
ccGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGTGATGATCATATTGCCCAGATCaa > 1:675800/1‑69 (MQ=255)
ccGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGTGATGATCATATTGCCCAGATCaa > 1:845635/1‑69 (MQ=255)
ccGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGTGATGATCATATTGCCCAGATCaa > 1:1384576/1‑69 (MQ=255)
ccGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGTGATGATCATATTGCCCAGATCaa > 1:1220782/1‑69 (MQ=255)
|
AGCGGCTTCGACGATCGCTTTTACGTTATCCAGCGACTGACGTGCCTGTGCAGCGACGTCTGCCGGTACTTCGCCCGTTTTCGGATTTACCGGGATCTGACCGGAGGTGATGATCATATTGCCCAGATCAA > minE/2912106‑2912236
|
| 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
