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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,573,836 |
A→G |
90.3% |
V200A (GTG→GCG) |
yihN ← |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,573,836 | 0 | A | G | 90.3%
| 121.0
/ 4.6
| 41 | V200A (GTG→GCG) | yihN | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base A (2/2); new base G (20/17); total (22/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01 |
CAGATAGTTTTGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGCAATCAC > W3110S.gb/3573770‑3573903
|
cAGATAGTTTTGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTc < 1:2940983/71‑1 (MQ=255)
cAGATAGTTTTGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTc < 1:538086/71‑1 (MQ=255)
aTAGTTTTGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAac > 1:2004304/1‑71 (MQ=255)
aTAGTTTTGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAac > 1:2319736/1‑71 (MQ=255)
ttttGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAacggac < 1:3160690/71‑1 (MQ=255)
ttttGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAacggac < 1:1965962/71‑1 (MQ=255)
ttGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAacggacgg > 1:112117/1‑71 (MQ=255)
ttGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAacggacg < 1:707558/70‑1 (MQ=255)
ttGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAacggacg < 1:3648212/70‑1 (MQ=255)
gTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGt < 1:96936/70‑1 (MQ=255)
gAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTc < 1:691882/71‑1 (MQ=255)
gTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCAtt < 1:718923/71‑1 (MQ=255)
aTACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAacggacgg > 1:3151742/1‑50 (MQ=255)
aTACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAacggacgg > 1:2955059/1‑50 (MQ=255)
aTACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAacggacgg > 1:2872187/1‑50 (MQ=255)
aTACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAacggacgg > 1:1401015/1‑50 (MQ=255)
aTACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCa > 1:1336990/1‑70 (MQ=255)
aTACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAg > 1:68580/1‑71 (MQ=255)
tACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTc < 1:3032778/40‑1 (MQ=255)
cTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGcc > 1:2329670/1‑36 (MQ=255)
ggTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACa > 1:2533245/1‑70 (MQ=255)
tttttCGATGCTCCGTCTTCTTTTTTCGCCTCAacggacg > 1:494633/1‑40 (MQ=255)
tttCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTcttctt > 1:2439248/1‑50 (MQ=255)
tttCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGaaaa > 1:1232902/1‑71 (MQ=255)
tttCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGaa > 1:1630220/1‑69 (MQ=255)
tGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataataa > 1:3659035/1‑71 (MQ=255)
tGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataataa < 1:2648508/71‑1 (MQ=255)
tGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataataa < 1:170107/71‑1 (MQ=255)
tGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataataa < 1:135235/71‑1 (MQ=255)
gCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataa > 1:803347/1‑67 (MQ=255)
cGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataataa < 1:2297741/66‑1 (MQ=255)
cGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGcc < 1:3090868/70‑1 (MQ=255)
ttcttTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACgg > 1:2773813/1‑71 (MQ=255)
ttcttTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataa > 1:3544869/1‑59 (MQ=255)
ttcttTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACg > 1:1454783/1‑70 (MQ=255)
cttTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACg < 1:1579566/68‑1 (MQ=255)
ttttCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGCAAt < 1:2548989/70‑1 (MQ=255)
ttttCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGCAAt < 1:2481585/70‑1 (MQ=255)
ttCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCa > 1:1227177/1‑37 (MQ=255)
ttCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCt > 1:671347/1‑60 (MQ=255)
tCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGCAATcac < 1:157137/70‑1 (MQ=255)
|
CAGATAGTTTTGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGCAATCAC > W3110S.gb/3573770‑3573903
|
| 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
