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 |
277,691 |
G→A |
48.9% |
L474L (CTG→TTG) |
cyoB ← |
cytochrome o ubiquinol oxidase subunit I |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 277,691 | 0 | G | A | 48.9%
| ‑1.6
/ 38.7
| 47 | L474L (CTG→TTG) | cyoB | cytochrome o ubiquinol oxidase subunit I |
| Reads supporting (aligned to +/- strand): ref base G (8/16); new base A (15/8); total (23/24) |
| Fisher's exact test for biased strand distribution p-value = 4.22e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGCATGGTGTGGAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGTTTACCCCAGG > minE/277627‑277759
|
aGCATGGTGTGGAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCa < 1:2300983/69‑1 (MQ=255)
aGCATGGTGTGGAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCa < 1:2871204/69‑1 (MQ=255)
aGCATGGTGTGGAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCa < 1:1565980/69‑1 (MQ=255)
aGCATGGTGTGGAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCa < 1:349768/69‑1 (MQ=255)
aGCATGGTGTGGAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCACATGAAGCCCAGCGCa < 1:372200/69‑1 (MQ=255)
aTGGTGTGGAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATa > 1:2104919/1‑68 (MQ=255)
aTGGTGTGGAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATAc > 1:1229413/1‑69 (MQ=255)
aTGGTGTGGAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATAc > 1:1230212/1‑69 (MQ=255)
gAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATCCCCATAAAGCCCAACGCATACAGCGGCa > 1:2457894/1‑68 (MQ=255)
gAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATCCCCATAAAGCCCAACGCATACAGCGGCa > 1:294297/1‑68 (MQ=255)
gAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGACATCCCCATAAAGCCCAACGCATACAGCGGCa > 1:2228543/1‑68 (MQ=255)
aCTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATACAGTGGCATaa > 1:1584434/1‑69 (MQ=255)
aCTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATACAGTGGCATaa > 1:2755710/1‑69 (MQ=255)
aCTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATACAGTGGCATaa > 1:839857/1‑69 (MQ=255)
tgctgGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACgaagaa > 1:1504726/1‑68 (MQ=255)
ggCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGcc < 1:1347073/67‑1 (MQ=255)
ggCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGcc < 1:1785909/67‑1 (MQ=255)
ggCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGcc < 1:3232909/67‑1 (MQ=255)
ggCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGcc < 1:601612/67‑1 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaagaa > 1:3075000/1‑55 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaagaa > 1:2479776/1‑55 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaagaa > 1:2414349/1‑55 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaagaa > 1:288183/1‑55 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaagaa > 1:3124969/1‑55 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaagaa > 1:3184512/1‑55 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaagaa > 1:1920311/1‑55 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaagaa > 1:1883551/1‑55 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaagaa > 1:1581516/1‑55 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaagaa > 1:502257/1‑55 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaagaa > 1:1238561/1‑55 (MQ=255)
gacgGGTCATCCCCATAAAGCCCAACGCATACAGCGGCATAAAGGCAACgaaga > 1:3270767/1‑54 (MQ=255)
gTCATGCCCATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATccagaaccag < 1:912561/69‑1 (MQ=255)
gTCATGCCCATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATccagaaccag < 1:2495186/69‑1 (MQ=255)
cATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAAcgcgcg < 1:1970500/69‑1 (MQ=255)
cATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAAcgcgcg < 1:1316688/69‑1 (MQ=255)
cATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAAcgcgcg < 1:1411905/69‑1 (MQ=255)
ataaaGCCCAACGCATACAGCTGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGt < 1:797998/66‑1 (MQ=255)
ataaaGCCCAACGCATACAGCGGCATAACGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGt < 1:2600628/66‑1 (MQ=255)
ataaaGCCCAACGCATACAGCGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGt < 1:1529480/66‑1 (MQ=255)
ataaaGCCCAACGCATACAGCGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGt < 1:1142164/66‑1 (MQ=255)
ataaaGCCCAACGCATACAGCGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGt < 1:70002/66‑1 (MQ=255)
ataaaGCCCAACGCATACAGCGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGt < 1:3290157/66‑1 (MQ=255)
ataaaGCCCAACGCATACAGCGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGt < 1:172430/66‑1 (MQ=255)
ataaaGCCCAACGCATACAGCGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGt < 1:1886031/66‑1 (MQ=255)
aTGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAAcgcgcg < 1:3425754/68‑1 (MQ=255)
tGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGtt < 1:124443/69‑1 (MQ=255)
aaGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGTTTa > 1:1017869/1‑69 (MQ=255)
gcgcATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGTTTACCCCAgg < 1:3346134/69‑1 (MQ=255)
gcgcATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGTTTACCCCAgg < 1:2145948/69‑1 (MQ=255)
gcgcATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGTTTACCCCAgg < 1:884966/69‑1 (MQ=255)
|
AGCATGGTGTGGAACTGCGGGTCAATCTGCTGGCTCAAACGACGGGTCATGCCCATGAAGCCCAGCGCATACAGTGGCATAAAGGCAACGAAGAAGCCGATGATCCAGAACCAGAACGCGCGTTTACCCCAGG > minE/277627‑277759
|
| 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
