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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,628,828 |
C→T |
39.0% |
*215* (TGA→TAA) |
ytjB ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,628,828 | 0 | C | T | 39.0%
| 49.0
/ 64.3
| 59 | *215* (TGA→TAA) | ytjB | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (23/13); new base T (7/16); total (30/29) |
| Fisher's exact test for biased strand distribution p-value = 1.69e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGTAAGAGTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGCGAT > W3110S.gb/4628763‑4628893
|
cGTAAGAGTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCActct > 1:2697756/1‑71 (MQ=255)
agagTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCttttt < 1:25220/71‑1 (MQ=255)
gTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTtct < 1:4557636/71‑1 (MQ=255)
agagATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCg > 1:5107001/1‑70 (MQ=255)
agaTGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCtt < 1:3926564/71‑1 (MQ=255)
gCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTtcttcc > 1:4829276/1‑71 (MQ=255)
aGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTtcttcctc > 1:3798904/1‑71 (MQ=255)
gCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTtcttcctctt < 1:1309084/71‑1 (MQ=255)
gCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTtcttcctctt < 1:1854915/71‑1 (MQ=255)
cGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTttcttc > 1:741657/1‑65 (MQ=255)
cGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTttcttc > 1:1497874/1‑65 (MQ=255)
cGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTttcttc > 1:1429605/1‑65 (MQ=255)
gTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTtcttcctcttcc > 1:237527/1‑71 (MQ=255)
gTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTtcttcctcttcc > 1:2345027/1‑71 (MQ=255)
aTGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCtttttt > 1:4142165/1‑49 (MQ=255)
ggACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCg > 1:3581153/1‑71 (MQ=255)
gACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCttt > 1:150620/1‑41 (MQ=255)
gACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCgg < 1:4952706/71‑1 (MQ=255)
gACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCgg < 1:3337996/71‑1 (MQ=255)
gACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCgg < 1:183977/71‑1 (MQ=255)
gACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTtc < 1:1165526/45‑1 (MQ=255)
gACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTtc < 1:1709247/45‑1 (MQ=255)
gACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTtc < 1:1785120/45‑1 (MQ=255)
gACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTtc < 1:2589679/45‑1 (MQ=255)
gACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTttctt > 1:1828834/1‑55 (MQ=255)
aTAACGATTTCCTTTCTTGTAGTAATGGGTTActct < 1:3416585/36‑1 (MQ=255)
aTAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGttt < 1:2101582/71‑1 (MQ=255)
tAACGATTTCCTTTCTTGTAGTAATGTGTTACTCTTTTTTCTCGCt < 1:1360648/46‑1 (MQ=255)
tAACGATTTCCTTTCTTGTAGTAATGGGTTACTCtt < 1:3806649/36‑1 (MQ=255)
tAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCt < 1:1111847/46‑1 (MQ=255)
tAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCt < 1:139498/46‑1 (MQ=255)
tAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCt < 1:495050/46‑1 (MQ=255)
aaCGATTTCCTTTCTTGTAGTAATGGGTTACTCttt > 1:732423/1‑36 (MQ=255)
aaCGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGc > 1:3181368/1‑71 (MQ=255)
aCGATTTCCTTTCTTGTAGTAATGGGTTACTCtttt > 1:2824059/1‑36 (MQ=255)
aCGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCgg > 1:398543/1‑59 (MQ=255)
aCGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCg > 1:3012839/1‑58 (MQ=255)
aCGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCg > 1:3739287/1‑58 (MQ=255)
cGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTg < 1:5018448/71‑1 (MQ=255)
gATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTgg < 1:668698/71‑1 (MQ=255)
gATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTttcttc < 1:314410/48‑1 (MQ=255)
tCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCa > 1:2267777/1‑55 (MQ=255)
ccTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTttctt > 1:1567519/1‑42 (MQ=255)
cTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGtt > 1:2784836/1‑70 (MQ=255)
tCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTaa < 1:4099052/69‑1 (MQ=255)
tCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCgg > 1:2559399/1‑54 (MQ=255)
tCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCt > 1:4500254/1‑60 (MQ=255)
tCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCt > 1:4558203/1‑60 (MQ=255)
tCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAAc < 1:1548143/70‑1 (MQ=255)
tCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACAGGTTTGCTGGCGGTTaa > 1:2196294/1‑69 (MQ=255)
gtagtaATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAg < 1:3940990/68‑1 (MQ=255)
tagtaATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAg > 1:902815/1‑71 (MQ=255)
taATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGc < 1:3856433/71‑1 (MQ=255)
taATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGc < 1:1183358/71‑1 (MQ=255)
aTGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGCg < 1:2302299/70‑1 (MQ=255)
aTGGGTCACTCTTTTTTCTCGCTTtcttcctcttc > 1:1040404/1‑35 (MQ=255)
aTGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGCGa > 1:1093558/1‑71 (MQ=255)
aTGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGCGa > 1:148717/1‑71 (MQ=255)
gggTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGCGAt < 1:923500/70‑1 (MQ=255)
|
CGTAAGAGTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGCGAT > W3110S.gb/4628763‑4628893
|
| 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
