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 F3 I0 R2
|
260 |
44.3 |
3360226 |
90.5% |
3041004 |
64.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,313,823 |
T→C |
44.4% |
E349G (GAA→GGA) |
yojL ← |
predicted thiamine biosynthesis lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,313,823 | 0 | T | C | 44.4%
| 17.3
/ 82.6
| 63 | E349G (GAA→GGA) | yojL | predicted thiamine biosynthesis lipoprotein |
| Reads supporting (aligned to +/- strand): ref base T (13/22); new base C (17/11); total (30/33) |
| Fisher's exact test for biased strand distribution p-value = 7.90e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.88e-01 |
TTAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACTGTGGTGACATCCAGGTTTTAAAGCTATCGCCTTCTTTGGTGA > W3110S.gb/2313754‑2313889
|
ttAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTc < 1:901366/71‑1 (MQ=255)
ttAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTc < 1:2673115/71‑1 (MQ=255)
ttAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTc < 1:2069943/71‑1 (MQ=255)
ttAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTc < 1:2575751/71‑1 (MQ=255)
ttAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTc < 1:2531107/71‑1 (MQ=255)
ttAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTc < 1:1604909/71‑1 (MQ=255)
ttAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTc < 1:570637/71‑1 (MQ=255)
ttAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTc < 1:2490370/71‑1 (MQ=255)
ttAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTc < 1:2455301/71‑1 (MQ=255)
tAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTc < 1:1099971/70‑1 (MQ=255)
gATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTc < 1:2395344/66‑1 (MQ=255)
aTAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGa > 1:470792/1‑70 (MQ=255)
aTAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTTAc < 1:2665162/71‑1 (MQ=255)
aTAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGAc < 1:2298571/71‑1 (MQ=255)
aTAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGAc < 1:1624453/71‑1 (MQ=255)
aTAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGAc < 1:2436535/71‑1 (MQ=255)
tGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCtttt > 1:2601497/1‑70 (MQ=255)
tGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCtttt > 1:243439/1‑70 (MQ=255)
tGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCtttt > 1:3103812/1‑70 (MQ=255)
tGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCtttt > 1:1745754/1‑70 (MQ=255)
tGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCtttt > 1:582907/1‑70 (MQ=255)
tGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCtttt > 1:809687/1‑70 (MQ=255)
tgccGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTa > 1:1904227/3‑70 (MQ=255)
gTCACCATCACGCAAAATCCATCAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACtgt < 1:2316802/71‑1 (MQ=255)
gTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACtgt < 1:2816816/71‑1 (MQ=255)
gTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACtgt < 1:2820752/71‑1 (MQ=255)
gTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACtgt < 1:3317332/71‑1 (MQ=255)
gTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACtgt < 1:562793/71‑1 (MQ=255)
gTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACtgt < 1:65695/71‑1 (MQ=255)
gTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACtgt < 1:94773/71‑1 (MQ=255)
gTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACtgt < 1:2401746/71‑1 (MQ=255)
gTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACtgt < 1:2276332/71‑1 (MQ=255)
gTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACtct < 1:2541482/71‑3 (MQ=255)
gTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACtgt < 1:1379237/71‑1 (MQ=255)
gTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACtgt < 1:1088455/71‑1 (MQ=255)
ccATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTgtggtg < 1:1484881/71‑1 (MQ=255)
ccATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTgtggtg < 1:1429613/71‑1 (MQ=255)
ccATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTgtggtg < 1:2112165/71‑1 (MQ=255)
ccATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTgtggtg < 1:2273958/71‑1 (MQ=255)
ccATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTgtggtg < 1:2467308/71‑1 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTaaa > 1:2163710/1‑61 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTaaa > 1:2813384/1‑61 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTaaa > 1:654687/1‑61 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTaaa > 1:1443843/1‑61 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTaa > 1:872914/1‑60 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:1107381/1‑70 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:1109211/1‑70 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:107429/1‑70 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:1073937/1‑70 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:530905/1‑70 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:3024434/1‑70 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:3186638/1‑70 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:2416626/1‑70 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:1995138/1‑70 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:2616993/1‑70 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:2404037/1‑70 (MQ=255)
aTCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTCCGCTGACAAGGAAGCTTTTAAACTGTGGTGa > 1:2412721/1‑70 (MQ=255)
cACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACTGTGGTGACAt > 1:1977263/1‑71 (MQ=255)
cACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACTGTGGTGACAt > 1:2962598/1‑71 (MQ=255)
cACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACTGTGGTGACAt > 1:2078210/1‑71 (MQ=255)
cACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACTGTGGTGACAt > 1:2083787/1‑71 (MQ=255)
cACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACTGTGGTGACAt > 1:2576312/1‑71 (MQ=255)
tAATTTTTTTCGCTGACAAGGAAGCTTTTAAACtgt < 1:778071/36‑1 (MQ=255)
tttcCGCTGACAAGGAAGCTTTTAAACTGTGGTGACATCCAGGTTTTAAAGCTATCGCCTTCTTTGGTGa < 1:703709/70‑1 (MQ=255)
|
TTAAGGATAGCCTTTAGGCTGCCCGGTCACCATCACGCAAAAACCAACAATCTTGCGCTTTAATTTTTTTCGCTGACAAGGAAGCTTTTAAACTGTGGTGACATCCAGGTTTTAAAGCTATCGCCTTCTTTGGTGA > W3110S.gb/2313754‑2313889
|
| 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
