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 |
1,802,101 |
G→A |
46.2% |
pseudogene (325/882 nt) |
ygaY → |
ECK2675:JW5428:b2681; predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,802,101 | 0 | G | A | 46.2%
| 9.4
/ 53.9
| 67 | pseudogene (325/882 nt) | ygaY | ECK2675:JW5428:b2681; predicted transporter |
| Reads supporting (aligned to +/- strand): ref base G (20/16); new base A (15/16); total (35/32) |
| Fisher's exact test for biased strand distribution p-value = 6.28e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.26e-01 |
GAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGCATTCTCTG > minE/1802037‑1802165
|
gAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATaa < 1:2458014/69‑1 (MQ=255)
gAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATaa < 1:1881254/69‑1 (MQ=255)
gAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATaa < 1:1367618/69‑1 (MQ=255)
gAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATaa < 1:3361188/69‑1 (MQ=255)
gAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATaa < 1:799380/69‑1 (MQ=255)
gAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATaa < 1:425745/69‑1 (MQ=255)
gAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATaa < 1:465103/69‑1 (MQ=255)
gAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATaa < 1:157932/69‑1 (MQ=255)
aTCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAAt < 1:235189/69‑1 (MQ=255)
aTCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAAt < 1:594284/69‑1 (MQ=255)
aTCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAAt < 1:778500/69‑1 (MQ=255)
aTCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAAt < 1:1445640/69‑1 (MQ=255)
aTCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAAt < 1:1438539/69‑1 (MQ=255)
aTCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAAt < 1:1151616/69‑1 (MQ=255)
tCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAAt < 1:3430170/68‑1 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:633429/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:392780/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:810909/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:3268214/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:839852/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:3267990/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:2990327/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:2505715/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:967647/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:1818858/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:155404/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:1877747/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:1758292/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAcc > 1:194237/1‑69 (MQ=255)
cACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGCATGTTTATCAGCAATAAGATCCTGCGCAc > 1:681787/1‑68 (MQ=255)
aCCCATAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGc > 1:1891050/1‑69 (MQ=255)
aCCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGt > 1:931964/1‑56 (MQ=255)
aCCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCcg > 1:703745/1‑61 (MQ=255)
aCCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGc > 1:1235625/1‑69 (MQ=255)
aCCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGc > 1:1776810/1‑69 (MQ=255)
aCCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGc > 1:2938213/1‑69 (MQ=255)
tgttgGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGtt > 1:823902/1‑58 (MQ=255)
tgttgGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGtt > 1:495075/1‑58 (MQ=255)
ccGTTTTCAGTATGTTTATCAGCGATAAAATTCTGAGTACCCGCGCGTTGCTGGGCTGCCTGACCttt > 1:2389815/1‑68 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:516103/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:427932/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:1678090/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:2318159/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:633522/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:96609/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:3261902/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:2238308/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:2378866/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:2604011/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:2549184/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:2507393/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:2499285/69‑1 (MQ=255)
ttttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:2092755/69‑1 (MQ=255)
tttCAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:1383905/68‑1 (MQ=255)
cAGCATGTTTATCAGCAATAAGATCCTGCGCACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCa < 1:2500797/65‑1 (MQ=255)
tATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAg < 1:2409653/69‑1 (MQ=255)
tGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGc > 1:157100/1‑68 (MQ=255)
tGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGc > 1:2176730/1‑68 (MQ=255)
tGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGCa > 1:3336088/1‑69 (MQ=255)
tGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGCa > 1:1614694/1‑69 (MQ=255)
tGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGCa > 1:29506/1‑69 (MQ=255)
tGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGCa > 1:1114947/1‑69 (MQ=255)
cAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACGTTTGCCAATTTCAGCATTCTCTg > 1:2237929/1‑69 (MQ=255)
cAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGCATtctc > 1:1426697/1‑67 (MQ=255)
cAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGCATTCTCTg > 1:624659/1‑69 (MQ=255)
cAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGCATTCTCTg > 1:941658/1‑69 (MQ=255)
cAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGCATTCTCTg > 1:1757147/1‑69 (MQ=255)
|
GAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTCAGCATTCTCTG > minE/1802037‑1802165
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
