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 |
1,680,919 |
G→A |
66.0% |
T1352I (ACC→ATC) |
yfhM ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,680,919 | 0 | G | A | 66.0%
| 27.8
/ 22.1
| 44 | T1352I (ACC→ATC) | yfhM | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (6/9); new base A (13/16); total (19/25) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CACTATTACGCGGCGTTTTCAGCGCCAGCGCAATCGCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTAAACCAGAAGCGGCATCTGCACGATGC > minE/1680854‑1680978
|
caCTATTACGCGGCGTTTTCAGCGCCAGCGCAATCGCTTCTTCACCACGCGTCGCATCACCCATGGt < 1:1249875/67‑1 (MQ=255)
caCTATTACGCGGCGTTTTCAGCGCCAGCGCAATCGCTTCTTCACCACGCGTCGCATCACCCATGGt < 1:3371011/67‑1 (MQ=255)
caCTATTACGCGGCGTTTTCAGCGCCAGCGCAATCGCTTCTTCACCACGCGTCGCATCACCCATGGt < 1:1896416/67‑1 (MQ=255)
aCTATTACGCGGCGTTTTCAGCGCCAGCGCAATCGCTTCTTCACCACGCGTCGCATCACACATGGt < 1:436991/66‑1 (MQ=255)
cgTTTTCAGCGCCAGCGCAATCGCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGcc < 1:1083867/69‑1 (MQ=255)
cgTTTTCAGCGCCAGCGCAATCGCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGcc < 1:718254/69‑1 (MQ=255)
cgTTTTCAGCGCCAGCGCAATCGCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGcc < 1:674664/69‑1 (MQ=255)
cgTTTTCAGCGCCAGCGCAATCGCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGcc < 1:1303267/69‑1 (MQ=255)
cgTTTTCAGCGCCAGCGCAATCGCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGcc < 1:2948916/69‑1 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGt > 1:94720/1‑68 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGt > 1:2687782/1‑68 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTa > 1:1828525/1‑69 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTa > 1:2131171/1‑69 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTa > 1:2270989/1‑69 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTa > 1:407259/1‑69 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTa > 1:2284485/1‑69 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTa > 1:1406105/1‑69 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTa > 1:3317017/1‑69 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTa > 1:792601/1‑69 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTa > 1:3219824/1‑69 (MQ=255)
cAATCGCTTCTTCACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTa > 1:1115345/1‑69 (MQ=255)
cAATCGCTTCTACACCACGCGTCGCATCACCCATGATTTTCAGCGCAAc > 1:2883168/1‑49 (MQ=255)
gCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTAAAcc > 1:1744996/1‑68 (MQ=255)
gCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTAAAcc > 1:1891171/1‑68 (MQ=255)
gCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTAAAcc > 1:423502/1‑68 (MQ=255)
gCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTAAAc > 1:2624362/1‑67 (MQ=255)
gCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTAAAc > 1:3349832/1‑67 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:1005799/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:735205/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:1169724/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:623903/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:621642/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:841447/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:910508/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:3209074/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:3172250/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:3159753/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:3001010/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:1597806/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:2613711/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:2556369/54‑1 (MQ=255)
cttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:2282643/54‑1 (MQ=255)
ttcACCACGCGTCGCATCACCCATGATTTTCAGCGCAACGCCAAGTTgcagca < 1:2407620/53‑1 (MQ=255)
cATGGTTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTAAACCAGAAGCGGCATCTGCACGATGc > 1:137290/1‑64 (MQ=255)
|
CACTATTACGCGGCGTTTTCAGCGCCAGCGCAATCGCTTCTTCACCACGCGTCGCATCACCCATGGTTTTCAGCGCAACGCCAAGTTGCAGCAGCGGTAAACCAGAAGCGGCATCTGCACGATGC > minE/1680854‑1680978
|
| 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
