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 F17 I0 R1
|
87 |
56.5 |
4283937 |
98.6% |
4223961 |
62.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,580,803 |
C→T |
16.7% |
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 | 16.7%
| 105.4
/ 13.0
| 42 | pseudogene (1987/2721 nt) | yjiV | ECK4334:JW5954:b4486; conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (13/22); new base T (3/4); total (16/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAAATGGGGGTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAACGAGTT > W3110S.gb/4580734‑4580873
|
gAAATGGGGGTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGc < 1:4215406/70‑1 (MQ=255)
gAAATGGGGGTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGc < 1:3116004/70‑1 (MQ=255)
aaTGGGGGTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCgg < 1:334431/71‑1 (MQ=255)
gggTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTgg < 1:747028/71‑1 (MQ=255)
gATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAg > 1:529039/1‑63 (MQ=255)
aTACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCt < 1:861847/70‑1 (MQ=255)
ccGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAAt > 1:3839346/1‑71 (MQ=255)
ccGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAAt < 1:3465237/71‑1 (MQ=255)
ccGATCGCGTGATGACGCTGGCCTCTCGCAGCCAG‑AGGCAACGATTCCGGGGTCGGAGTGGCACCTGa > 1:3109149/1‑68 (MQ=255)
cGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGTCGGAGTGGCACCTGAAt > 1:3924137/1‑70 (MQ=255)
aTCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGAc > 1:4109353/1‑71 (MQ=255)
atgaCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGTCGGAGTGGCACCTGAATGACGAACtggt < 1:3072257/71‑1 (MQ=255)
atgaCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACtgg < 1:3455244/70‑1 (MQ=255)
tgaCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACg < 1:3153630/63‑1 (MQ=255)
tgaCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACg < 1:1075911/63‑1 (MQ=255)
gaCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACtggtg > 1:2193213/1‑70 (MQ=255)
aCGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGTCGGAGTGGCACCTGAATGACGAACTggtggt < 1:4246986/71‑1 (MQ=255)
cGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGa > 1:1867408/1‑61 (MQ=255)
gCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACtg < 1:2802853/64‑1 (MQ=255)
cTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCg < 1:4205371/71‑1 (MQ=255)
tGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCg > 1:2306059/1‑70 (MQ=255)
ccTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGt < 1:1446999/68‑1 (MQ=255)
tcGCAGCCAGCAGGCAACGATTCCGGGGTCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCg > 1:4084892/1‑71 (MQ=255)
gCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGtctc < 1:1370697/68‑1 (MQ=255)
gCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGtctc < 1:2219368/68‑1 (MQ=255)
gCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCgg < 1:2507881/70‑1 (MQ=255)
agcagGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTtata > 1:2856725/1‑69 (MQ=255)
gcagGCAACGATTCCGGGGTCGGAGTGGCACCTGAATGACGAACTGGTGGTGCg < 1:2174142/54‑1 (MQ=255)
agGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACg > 1:639497/1‑71 (MQ=255)
ggCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACgg > 1:247259/1‑71 (MQ=255)
gCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATaaaa < 1:3074998/67‑1 (MQ=255)
aaCGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACgg > 1:4141674/1‑68 (MQ=255)
ccGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACtggt < 1:4179065/40‑1 (MQ=255)
aCGATTCCGGGGTCGGAGTGGCACCTGAATGACGAACTggtggt < 1:949382/44‑1 (MQ=255)
cGATTCCGTGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGaa > 1:3638174/1‑71 (MQ=255)
cGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGaa > 1:3022199/1‑71 (MQ=255)
aTTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGtt < 1:2826181/55‑1 (MQ=255)
ccGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGa < 1:1692163/70‑1 (MQ=255)
ccGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGa < 1:1272822/70‑1 (MQ=255)
ggggCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAACg < 1:3975184/71‑1 (MQ=255)
ggggCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAACg < 1:3152458/71‑1 (MQ=255)
gggCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAACg < 1:1812370/70‑1 (MQ=255)
ggCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGt < 1:1206509/58‑1 (MQ=255)
ggCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAACGAg > 1:3339559/1‑71 (MQ=255)
ccGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAACGAGtt < 1:3006134/71‑1 (MQ=255)
|
GAAATGGGGGTTGATACCGATCGCGTGATGACGCTGGCCTCTCGCAGCCAGCAGGCAACGATTCCGGGGCCGGAGTGGCACCTGAATGACGAACTGGTGGTGCGTAGTCTCGGTTATAAAACGGTAGAACTGAACGAGTT > W3110S.gb/4580734‑4580873
|
| 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
