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 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,191,865 |
G→A |
7.5% |
A116T (GCC→ACC) |
yqiK → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,191,865 | 0 | G | A | 7.5%
| 168.9
/ 3.5
| 53 | A116T (GCC→ACC) | yqiK | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (30/19); new base A (2/2); total (32/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01 |
GATGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAATTTGT > W3110S.gb/3191805‑3191932
|
gATGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCt < 1:346705/71‑1 (MQ=255)
aTGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTg > 1:318873/1‑60 (MQ=255)
gtagtaGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTACCCAGACGCTggg > 1:3885540/1‑71 (MQ=255)
gtagtCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTg < 1:1459574/66‑1 (MQ=255)
tagtCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCaa > 1:634368/1‑71 (MQ=255)
gtCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACg > 1:3958238/1‑71 (MQ=255)
gCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCa < 1:2645053/70‑1 (MQ=255)
gCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCAc > 1:2822749/1‑71 (MQ=255)
ctttctttGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCAcc < 1:3819344/71‑1 (MQ=255)
ctttctttGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCAcc < 1:406874/71‑1 (MQ=255)
ctttctttGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTACCCAGACGCTGGGGCAACGCAcc > 1:2366694/1‑71 (MQ=255)
tttctttGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCAccc > 1:3372799/1‑71 (MQ=255)
tgtgCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGc > 1:1561693/1‑71 (MQ=255)
tgCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTg < 1:160352/65‑1 (MQ=255)
tgCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGcc < 1:1625306/70‑1 (MQ=255)
cggTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTTGGGCAACGCACCCTGTCGCCTg > 1:554390/2‑69 (MQ=255)
gTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGa < 1:2688753/71‑1 (MQ=255)
aaaCCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTg < 1:3058017/57‑1 (MQ=255)
aaaCCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGa > 1:3433628/1‑68 (MQ=255)
aaaCCTTCAGTAGAAGGGATTGCCACCGCTACCCAGACGCTGGGGCAACGCACCCt < 1:1852785/56‑1 (MQ=255)
aaaCCTTCAGTAGAAGGGATTGCAACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACt > 1:279934/1‑70 (MQ=255)
aCCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTAc > 1:1835738/1‑71 (MQ=255)
ccTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACg > 1:3671119/1‑71 (MQ=255)
tCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGcc > 1:559314/1‑56 (MQ=255)
tCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTAt > 1:178825/1‑71 (MQ=255)
aGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgt < 1:331341/71‑1 (MQ=255)
tAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgttg < 1:2728816/71‑1 (MQ=255)
gAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCa < 1:2975207/40‑1 (MQ=255)
gAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGc > 1:3239210/1‑49 (MQ=255)
gAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgttggt > 1:4590199/1‑71 (MQ=255)
gAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgttgg < 1:3235043/70‑1 (MQ=255)
aaGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgttggtt > 1:1863504/1‑71 (MQ=255)
aGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgttggtt > 1:1734049/1‑70 (MQ=255)
aGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgttggtt > 1:1613444/1‑70 (MQ=255)
gggATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgttggttg > 1:1512944/1‑70 (MQ=255)
gggATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATgttggttg > 1:2854374/1‑70 (MQ=255)
ttGCCACCGCTGCCCAGCCGCTGGGGCAACGCACCCTGTCGcc > 1:3855892/1‑43 (MQ=255)
ttGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGa > 1:2199982/1‑70 (MQ=255)
gCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGa > 1:3481855/1‑47 (MQ=255)
gCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATa > 1:2881908/1‑70 (MQ=255)
ccACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTTAAGACTTACGTATGTTGGTTGAAGATaa < 1:1402185/70‑1 (MQ=255)
ccACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATaaa < 1:2341379/71‑1 (MQ=255)
ccACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATaaa < 1:3994330/71‑1 (MQ=255)
cACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAAt > 1:2782248/1‑71 (MQ=255)
aCCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTa > 1:3193218/1‑52 (MQ=255)
aCCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAAtt > 1:3522402/1‑71 (MQ=255)
ccGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAAttt < 1:4459772/71‑1 (MQ=255)
ccGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAAttt < 1:468527/71‑1 (MQ=255)
ccGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCATGAAGACTTACGTATGTTGGTTGAAGATAAAttt > 1:3668266/1‑71 (MQ=255)
ccGCTACCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAAttt < 1:927860/71‑1 (MQ=255)
cGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAATTTg > 1:3817169/1‑71 (MQ=255)
gCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAATTTGt > 1:534540/1‑71 (MQ=255)
gCTGACCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAATTTGt > 1:3528166/1‑71 (MQ=255)
cTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGt < 1:3267259/47‑1 (MQ=255)
gCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGAt < 1:3343082/60‑1 (MQ=255)
|
GATGTAGTAGTCGCTTTCTTTGTGCGGGTAAAACCTTCAGTAGAAGGGATTGCCACCGCTGCCCAGACGCTGGGGCAACGCACCCTGTCGCCTGAAGACTTACGTATGTTGGTTGAAGATAAATTTGT > W3110S.gb/3191805‑3191932
|
| 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
