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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,491,067 |
G→A |
66.7% |
V56V (GTG→GTA) |
yjgP → |
conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,491,067 | 0 | G | A | 66.7%
| 48.2
/ 44.1
| 48 | V56V (GTG→GTA) | yjgP | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base G (12/4); new base A (16/16); total (28/20) |
| Fisher's exact test for biased strand distribution p-value = 1.27e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.94e-01 |
CCTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTGCCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCGGGCTGCTGATGACGCTGGG > W3110S.gb/4491001‑4491129
|
ccTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTGc > 1:1011607/1‑68 (MQ=255)
cGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGa < 1:1175212/69‑1 (MQ=255)
ggCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTGCCgg > 1:3196280/1‑67 (MQ=255)
ggCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTGCCGGa > 1:840343/1‑68 (MQ=255)
ggCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGaa > 1:2941811/1‑69 (MQ=255)
ggTTGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCa > 1:607164/1‑69 (MQ=255)
gTTGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAg > 1:3410086/1‑69 (MQ=255)
ttGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAg < 1:2008947/68‑1 (MQ=255)
tGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTGCCGGa > 1:577553/1‑57 (MQ=255)
tGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTGCCGGa > 1:2427154/1‑57 (MQ=255)
gACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCTCa < 1:1684264/65‑1 (MQ=255)
gACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCa < 1:1881092/65‑1 (MQ=255)
gACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCa < 1:325634/65‑1 (MQ=255)
cGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTGCCGGAAATGGCGCAGCTTa < 1:2952563/68‑1 (MQ=255)
cGATATTCCGGCGAATCTTGTGCTCTCCCTTCTCGGGTTGGTCGTACCGGAAATGGCGCAGCTTATCCt < 1:3481166/69‑1 (MQ=255)
cGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCt < 1:3607162/69‑1 (MQ=255)
atTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGcc > 1:1897896/1‑68 (MQ=255)
ttCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGc < 1:1714583/66‑1 (MQ=255)
ccGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGgcg > 1:2680552/1‑51 (MQ=255)
ccGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTa > 1:188805/1‑58 (MQ=255)
ccGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTa > 1:999437/1‑69 (MQ=255)
ccGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTa > 1:3345005/1‑69 (MQ=255)
cGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGcc < 1:2444246/69‑1 (MQ=255)
gAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGcc < 1:947441/68‑1 (MQ=255)
tCTGGTGCTCTCCCTTCTCGGGTTGGGCGTGCCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGtt > 1:2183417/1‑69 (MQ=255)
tGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTaa > 1:2124324/1‑57 (MQ=255)
tGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAg > 1:275035/1‑58 (MQ=255)
tGCTCTCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAg > 1:17819/1‑58 (MQ=255)
ctctCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCggg > 1:16612/1‑69 (MQ=255)
ctctCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCggg > 1:2345201/1‑69 (MQ=255)
ctctCCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCggg > 1:2576912/1‑69 (MQ=255)
ctcCCTTCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCGGgct > 1:2851311/1‑69 (MQ=255)
ccTTCTCGGGTTGGGCGTGCCGGAAATGGCGCAGCt > 1:922153/1‑36 (MQ=255)
ccTTCTCGGGTTGGGCGTGCCGGAAATGGCGCAGCt > 1:2623167/1‑36 (MQ=255)
ccTTCTCGGGTTGGGCGTGCCGGAAATGGCGCAGCt > 1:572253/1‑36 (MQ=255)
ttCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCTTGCCATTAAGCCTGt < 1:473867/54‑1 (MQ=255)
ttCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGt < 1:2261231/54‑1 (MQ=255)
ttCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGt < 1:2113462/54‑1 (MQ=255)
ttCTCGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCGGgctgct < 1:3558551/67‑1 (MQ=255)
tctcGGGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCGGGCTGCtgat < 1:3592060/69‑1 (MQ=255)
ctcGGGTTGGGCGTGCCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCGGGCTGCtgatg > 1:1325772/1‑69 (MQ=255)
tcGTGTTGGGCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGt < 1:2455764/51‑1 (MQ=255)
tGGGCGTGCCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCgg < 1:489850/52‑1 (MQ=255)
tGGGCGTGCCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCgg < 1:779692/52‑1 (MQ=255)
tGGGCGTGCCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCgg < 1:1388554/52‑1 (MQ=255)
gggCGTACCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCGGGCTGCtgat > 1:3385383/1‑60 (MQ=255)
ggCGTGCCGGAAATGGCGCAGCTTATCCTGCCAtt > 1:843846/1‑35 (MQ=255)
ggCGTGCCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCGGGCTGCTGATGACGCTggg > 1:3132126/1‑68 (MQ=255)
|
CCTCGGCGCAGCGGTTGACGGCGATATTCCGGCGAATCTGGTGCTCTCCCTTCTCGGGTTGGGCGTGCCGGAAATGGCGCAGCTTATCCTGCCATTAAGCCTGTTCCTCGGGCTGCTGATGACGCTGGG > W3110S.gb/4491001‑4491129
|
| 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
