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 |
2,239,637 |
A→T |
53.3% |
P275P (CCT→CCA) |
zraS ← |
sensory histidine kinase in two‑component regulatory system with ZraR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,239,637 | 0 | A | T | 53.3%
| ‑1.0
/ 50.2
| 45 | P275P (CCT→CCA) | zraS | sensory histidine kinase in two‑component regulatory system with ZraR |
| Reads supporting (aligned to +/- strand): ref base A (7/14); new base T (5/19); total (12/33) |
| Fisher's exact test for biased strand distribution p-value = 5.01e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.05e-01 |
TAAACGGTCGGCCTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGAAAGTG > minE/2239580‑2239686
|
tAAACGGTCGGCCTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTc > 1:1110570/1‑69 (MQ=255)
tAAACGGTCGGCCTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTc > 1:737107/1‑69 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:2555350/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:940454/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:910622/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:75288/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:696294/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:681090/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:565001/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:3223709/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:3065045/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:2710850/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:2644933/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:1007988/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:1186291/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:2045365/63‑1 (MQ=255)
aCGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTACTCCCCCTGCTGgcgcgcg < 1:2264090/63‑1 (MQ=255)
cGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:2362985/62‑1 (MQ=255)
cGGTCAGCTTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:2668752/62‑1 (MQ=255)
gTCGGCCTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCaa > 1:1036475/1‑68 (MQ=255)
tCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCTGgcgcgcg < 1:377146/49‑1 (MQ=255)
aCCTGCGCCAGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTa > 1:3382857/1‑69 (MQ=255)
aCCTGCGCCAGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTAGCCAGTCCTTTa > 1:732969/1‑69 (MQ=255)
aGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGaa < 1:170326/69‑1 (MQ=255)
aGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGaa < 1:1081666/69‑1 (MQ=255)
aGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGaa < 1:1157260/69‑1 (MQ=255)
aGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGaa < 1:687112/69‑1 (MQ=255)
aGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGaa < 1:553466/69‑1 (MQ=255)
aGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGaa < 1:2183390/69‑1 (MQ=255)
aGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGaa < 1:3000903/69‑1 (MQ=255)
aGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATAGAGGaa < 1:325727/69‑1 (MQ=255)
gTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGaa < 1:3088118/68‑1 (MQ=255)
gTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGaa < 1:2501904/68‑1 (MQ=255)
gATGCGCTTCTCCCCCTGCTGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGAAAGTg < 1:2175706/69‑1 (MQ=255)
gATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGAAAGt > 1:2338035/1‑68 (MQ=255)
gATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGAAAGTg > 1:1257739/1‑69 (MQ=255)
gATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGAAAGTg < 1:2618169/69‑1 (MQ=255)
gATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGAAAGTg < 1:1789626/69‑1 (MQ=255)
gATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGAAAGTg < 1:2127210/69‑1 (MQ=255)
tGCGCTTCTCCCCCTGCTGGCGCGCGTTCGGCAAAGTAt > 1:1204145/1‑39 (MQ=38)
tGCGCTTCTCCCCCTGCTGGCGCGCGTTCGGCAAAGTAt > 1:1829508/1‑39 (MQ=38)
tGCGCTTCTCCCCCTGCTGGCGCGCGTTCGGCAAAGTAt > 1:2549596/1‑39 (MQ=38)
tGCGCTTCTCCCCCTGCTGGCGCGCGTTCGGCAAAGTAt > 1:1171044/1‑39 (MQ=38)
agcgcTTCTCCCCCTGCTGGCGCGCGTTCGGCAAAGTAt > 1:1274620/2‑39 (MQ=37)
cTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGaa < 1:2936556/50‑1 (MQ=255)
|
TAAACGGTCGGCCTCTTTCGCCATCACCTGCGCCAGTTGATGCGCTTCTCCCCCTGCAGGCGCGCGCTCGGCAAAGTATTTCGCCAGTCCTTTAATCGAGGAAAGTG > minE/2239580‑2239686
|
| 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
