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 |
4,580,803 |
C→T |
30.4% |
pseudogene (1987/2721 nt) |
yjiV → |
ECK4334:JW5954:b4486; conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,580,803 | 0 | C | T | 30.4%
| 69.5
/ 30.5
| 46 | pseudogene (1987/2721 nt) | yjiV | ECK4334:JW5954:b4486; conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (15/17); new base T (4/10); total (19/27) |
| Fisher's exact test for biased strand distribution p-value = 3.35e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAATGGGGGTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAACGA > W3110S.gb/4580735‑4580870
|
aaaTGGGGGTTGATACCGATCCCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGTCg < 1:4715790/71‑1 (MQ=255)
aaTGGGGGTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCgg < 1:5133583/71‑1 (MQ=255)
ggTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGc < 1:2839193/71‑1 (MQ=255)
ggTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGc < 1:488591/71‑1 (MQ=255)
gTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCgg < 1:2319301/64‑1 (MQ=255)
ttGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCgg < 1:111938/63‑1 (MQ=255)
aTACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTg < 1:553943/71‑1 (MQ=255)
aCCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGaa > 1:2954933/1‑71 (MQ=255)
ccGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGt > 1:1735183/1‑60 (MQ=255)
tgatgaCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGTCg < 1:4458993/47‑1 (MQ=255)
tgatgaCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGTCg < 1:1641480/47‑1 (MQ=255)
tgatgaCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCa < 1:4823887/55‑1 (MQ=255)
tgatgaCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACtg < 1:3578196/71‑1 (MQ=255)
tgaCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACtggtg < 1:829997/71‑1 (MQ=255)
gaCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCAGCTGAATGACGAACt > 1:2542069/1‑66 (MQ=255)
cGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGTCGGAGTGGCACCTGAATGACGAACTGgtggtg < 1:4105810/71‑1 (MQ=255)
cGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGTCGGAGCGGCACCTGAATGACGAACTGgtggtg < 1:3587083/71‑1 (MQ=255)
tGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGTCgg < 1:2099593/39‑1 (MQ=255)
gCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTa < 1:2635969/70‑1 (MQ=255)
gCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTa < 1:4181229/70‑1 (MQ=255)
gCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTa < 1:3596162/70‑1 (MQ=255)
cGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCgg > 1:4483438/1‑71 (MQ=255)
cagccagcAGGCAACGATTCCGGGGCCGGAGTGGCACCTGaa > 1:5088491/1‑42 (MQ=255)
gccagcAGGCAACGATTCCGGGGTCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTtat < 1:3727055/71‑1 (MQ=255)
ccagcAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTtata < 1:2680901/71‑1 (MQ=255)
gcagTCAACGATTCCGGGGTCGGAGTGGCACCTGAATGACGAACtgg < 1:2405277/47‑1 (MQ=255)
gcagGCAACGATTCCGGGGTCGGAGTGGCACCTGAATGACGAACtgg < 1:2411170/47‑1 (MQ=255)
cagGCAACGATTCCGGGGTCGGAGTGGCACCTGAATGACGAACTGgtggtg < 1:423347/51‑1 (MQ=255)
cAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACtggt < 1:3274631/43‑1 (MQ=255)
cAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTa > 1:2177601/1‑51 (MQ=255)
aaCGATTCCGGTGTCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACgg > 1:3320680/1‑68 (MQ=255)
aaCGATTCCGGGGCCGGAGTGGCACCTGAATGACGAAc > 1:3454276/1‑38 (MQ=255)
aaCGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTa > 1:3530094/1‑50 (MQ=255)
aaCGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTa > 1:4561791/1‑50 (MQ=255)
aaCGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTa > 1:2549984/1‑50 (MQ=255)
aaCGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTta > 1:1285593/1‑60 (MQ=255)
aaCGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACgg > 1:3111837/1‑68 (MQ=255)
gATTCCGGGGTCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAAc > 1:3438535/1‑71 (MQ=255)
gATTCCGGGGTCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAAc > 1:705229/1‑71 (MQ=255)
gATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAAc > 1:4752427/1‑71 (MQ=255)
gATTCAGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAAc > 1:510482/1‑71 (MQ=255)
tCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGtc > 1:4694576/1‑47 (MQ=255)
ccGGGGTCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTtata > 1:2727467/1‑55 (MQ=255)
cGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAAc < 1:1844891/71‑1 (MQ=255)
gggCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAACGa < 1:4920980/71‑1 (MQ=255)
ggCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAACGa < 1:252099/70‑1 (MQ=255)
|
AAATGGGGGTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAACGA > W3110S.gb/4580735‑4580870
|
| 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
