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 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,525,582 |
A→G |
30.9% |
T188A (ACC→GCC) |
yncE → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,525,582 | 0 | A | G | 30.9%
| 50.9
/ 34.2
| 42 | T188A (ACC→GCC) | yncE | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (24/5); new base G (7/6); total (31/11) |
| Fisher's exact test for biased strand distribution p-value = 6.64e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01 |
TGATTTGGGTCGTTGATGGCGGGAATATCAAACTGAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTAACGCTGACGGCGAATTGAT > W3110S.gb/1525514‑1525646
|
tGATTTGGGTCGTTGATGGCGGGAATATCAAACTGAAAACCGCCATCCAGAACACCGGTAAAATGAGTGcc > 1:1894991/1‑71 (MQ=255)
aTTTGGGTCGTTGATGGCGGGAATATCAAACTGAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCgg > 1:3885487/1‑71 (MQ=255)
ttGATGGCGGGAATATCAAACTGAAAACCGCCATCCAGAACACCGGTAAAATGAGTGCCGGTCTGGCGCTg < 1:942694/71‑1 (MQ=255)
ggCGGGAATATCAAACTGAAAACCGCCATCCAGAACACCGGTAAAATAAGTGCCGGTCTGGCGCTGGATAg > 1:2169180/1‑71 (MQ=255)
ggAATATCAAACTGAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCg > 1:4422793/1‑69 (MQ=255)
ggAATATCAAACTGAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCg > 1:2650071/1‑69 (MQ=255)
tCAAACTGAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCa > 1:3257545/1‑69 (MQ=255)
aaaCTGAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCGGTc > 1:5116118/1‑46 (MQ=255)
aaaCTGAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCt > 1:3751874/1‑47 (MQ=255)
tGAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTgg > 1:231115/1‑45 (MQ=255)
tGAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTgg > 1:2604952/1‑45 (MQ=255)
gAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCtt > 1:3840078/1‑70 (MQ=255)
gAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCt > 1:4845602/1‑69 (MQ=255)
aaaaCCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCtt < 1:657281/69‑1 (MQ=255)
aaaCCGCCATCCAGAACACCGGTAAAATGAGTGCCGGTCTGGCGCTGGATAGCGaa < 1:493928/56‑1 (MQ=255)
aaaCCGCCATCCAGAACACCGGTAAAATGAGTGCCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCtt < 1:181953/68‑1 (MQ=255)
aCCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTacac > 1:2280968/1‑71 (MQ=255)
cGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTAcacca > 1:4398835/1‑71 (MQ=255)
cATCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACt < 1:4849124/70‑1 (MQ=255)
tCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACt < 1:4966127/68‑1 (MQ=255)
cAGAACACCGGTAAAATGAGTGCCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTacac < 1:875928/62‑1 (MQ=255)
cAGAACACCGGTAAAATGAGTGCCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTAACGc > 1:952461/1‑71 (MQ=255)
cAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCaaa > 1:128725/1‑51 (MQ=255)
cAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCaaa > 1:3834822/1‑51 (MQ=255)
cAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCaaa > 1:3031102/1‑51 (MQ=255)
cAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTaa > 1:4340067/1‑68 (MQ=255)
cAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTAACGc > 1:279870/1‑71 (MQ=255)
aGAACACCGGTAAAATGAGTGCCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTAACGCt < 1:154435/71‑1 (MQ=255)
gAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTaa > 1:3564767/1‑66 (MQ=255)
acacCGGTAAAATCAGTGCCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTAACGCTGAc > 1:532445/1‑71 (MQ=255)
acCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGc < 1:702926/36‑1 (MQ=255)
ccGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTAACGCTGACGGc > 1:1854215/1‑71 (MQ=255)
ggTAAAATGAGTGCCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTAACGCTGACGGCg > 1:806883/1‑70 (MQ=255)
gTAAAATGAGTGCCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTaca > 1:94183/1‑51 (MQ=255)
aaaaTGAGTGCCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTAACGCTGACGGCGAAtt > 1:4271486/1‑71 (MQ=255)
aTGAGTGCCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTAACGCTGACGGCGAATTGAt < 1:2693024/71‑1 (MQ=255)
gAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAAc > 1:1710785/1‑35 (MQ=255)
gAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGt > 1:4785929/1‑37 (MQ=255)
gAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGt > 1:845856/1‑37 (MQ=255)
aGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTa > 1:4545428/1‑41 (MQ=255)
aGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTa > 1:2447960/1‑41 (MQ=255)
tACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTAACGCTGACGGCg < 1:3171308/59‑1 (MQ=255)
|
TGATTTGGGTCGTTGATGGCGGGAATATCAAACTGAAAACCGCCATCCAGAACACCGGTAAAATGAGTACCGGTCTGGCGCTGGATAGCGAAGGCAAACGTCTTTACACCACTAACGCTGACGGCGAATTGAT > W3110S.gb/1525514‑1525646
|
| 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
