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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
432,675 |
T→C |
55.0% |
S347S (TCT→TCC) |
ybfM → |
predicted outer membrane porin |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 432,675 | 0 | T | C | 55.0%
| 8.6
/ 38.3
| 51 | S347S (TCT→TCC) | ybfM | predicted outer membrane porin |
| Reads supporting (aligned to +/- strand): ref base T (14/9); new base C (20/8); total (34/17) |
| Fisher's exact test for biased strand distribution p-value = 5.53e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.48e-01 |
CGTATGACTCCAACCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGTATGACCTGAAAAACTGGA > minE/432613‑432739
|
cGTATGACTCCAACCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTc < 1:125533/69‑1 (MQ=255)
tATGACTCCAACCTACGCTTCTTCCAACGGCCGCCTGGATATCTGGTGGGATAACCGTTCCGACTTCaa < 1:2289166/69‑1 (MQ=255)
tATGACTCCAACCTACGCTTCTTCCAACGGCCGCCTGGATATCTGGTGGGATAACCGTTCCGACTTCaa < 1:773046/69‑1 (MQ=255)
tATGACTCCAACCTACGCTTCTTCCAACGGCCGCCTGGATATCTGGTGGGATAACCGTTCCGACTTCaa < 1:653677/69‑1 (MQ=255)
tATGACTCCAACCTACGCTTCTTCCAACGGCCGCCTGGATATCTGGTGGGATAACCGTTCCGACTTCaa < 1:2381542/69‑1 (MQ=255)
tATGACTCCAACCTACGCTTCTTCCAACGGCCGCCTGGATATCTGGTGGGATAACCGTTCCGACTTCaa < 1:1689617/69‑1 (MQ=255)
tATGACTCCAACCTACGCTTCTTCCAACGGCCGCCTGGATATCTGGTGGGATAACCGTTCCGACTTCaa < 1:3412185/69‑1 (MQ=255)
tATGACTCCAACCTACGCTTCTTCCAACGGCCGCCTGGATATCTGGTGGGATAACCGTTCCGACTTCaa < 1:2854214/69‑1 (MQ=255)
aTGACTCCAACCTACGCTTCTTCCAACGGCCGCCTGGATATCTGGTGGGATAACCGTTCCGACTTCaa < 1:2089688/68‑1 (MQ=255)
aCTCCAACCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATTACCGTTCTGACTTCAACGcc > 1:1992772/1‑69 (MQ=255)
aCTCCAACCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGcc > 1:3284792/1‑69 (MQ=255)
aCTCCAACCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGcc > 1:2272246/1‑69 (MQ=255)
aCTCCAACCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGcc > 1:2579883/1‑69 (MQ=255)
aCTCCAACCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGcc > 1:18447/1‑69 (MQ=255)
aCTCCAACCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGcc > 1:3300665/1‑69 (MQ=255)
aCTCCAACCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGcc > 1:1447476/1‑69 (MQ=255)
aCCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGCCAACgg > 1:2705113/1‑68 (MQ=255)
aCCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGCCAACgg > 1:2053648/1‑68 (MQ=255)
aCCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGCCAACgg > 1:1251171/1‑68 (MQ=255)
aCGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGCCAACGGCGa > 1:540579/1‑67 (MQ=255)
cTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTc < 1:1514336/50‑1 (MQ=255)
tatCTGGTGGGATAACCGTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCTATg < 1:1224284/67‑1 (MQ=255)
tatCTGGTGGGATAACCGTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATg < 1:3085726/67‑1 (MQ=255)
tatCTGGTGGGATAACCGTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATg < 1:2316245/67‑1 (MQ=255)
tatCTGGTGGGATAACCGTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATg < 1:1006345/67‑1 (MQ=255)
tatCTGGTGGGATAACCGTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATg < 1:2074595/67‑1 (MQ=255)
tatCTGGTGGGATAACCGTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATg < 1:1410188/67‑1 (MQ=255)
aTAACCGTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGTATGACCTGaaaa < 1:2114058/69‑1 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:970967/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:925147/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:919787/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:880008/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:75045/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:734587/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:1635100/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:366784/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:1694093/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:3400123/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:3319981/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:1731995/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:1831139/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:3260583/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:1897215/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:3027997/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:196382/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:2681189/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:202042/1‑55 (MQ=255)
aaCCGTTCCGACTTCAACGCTAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGt > 1:2477765/1‑55 (MQ=255)
gTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGTATGACCTGAAAAACTGGa > 1:1513364/1‑69 (MQ=255)
gTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGTATGACCTGAAAAACTGGa > 1:684066/1‑69 (MQ=255)
gTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGTATGACCTGAAAAACTGGa > 1:2009089/1‑69 (MQ=255)
|
CGTATGACTCCAACCTACGCTTCCTCAAACGGTCGCCTGGATATCTGGTGGGATAACCGTTCTGACTTCAACGCCAACGGCGAAAAAGCGGTCTTCTTCGGTGCGATGTATGACCTGAAAAACTGGA > minE/432613‑432739
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
