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 |
1,359,918 |
A→G |
43.7% |
S172S (TCT→TCC) |
yehD ← |
predicted fimbrial‑like adhesin protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,359,918 | 0 | A | G | 43.7%
| 11.5
/ 49.6
| 64 | S172S (TCT→TCC) | yehD | predicted fimbrial‑like adhesin protein |
| Reads supporting (aligned to +/- strand): ref base A (7/29); new base G (10/18); total (17/47) |
| Fisher's exact test for biased strand distribution p-value = 1.65e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01 |
TGTTTATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTAAA > minE/1359856‑1359980
|
tGTTTATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGAt < 1:1172455/69‑1 (MQ=255)
tGTTTATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGAt < 1:2359339/69‑1 (MQ=255)
tGTTTATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGAt < 1:157809/69‑1 (MQ=255)
tttATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGAt > 1:786952/1‑67 (MQ=255)
tttATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATaa < 1:2583832/69‑1 (MQ=255)
tttATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATaa < 1:1833193/69‑1 (MQ=255)
tttATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATaa < 1:2196346/69‑1 (MQ=255)
tttATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATaa < 1:1704120/69‑1 (MQ=255)
tttATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATaa < 1:2209535/69‑1 (MQ=255)
tttATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATaa < 1:1541695/69‑1 (MQ=255)
tttATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATaa > 1:2375997/1‑69 (MQ=255)
tttATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATaa < 1:2617372/69‑1 (MQ=255)
tttATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATaa < 1:2665857/69‑1 (MQ=255)
tttATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATaa < 1:380687/69‑1 (MQ=255)
ttattaCCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATaa < 1:2766870/68‑1 (MQ=255)
tattaCCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATAaca < 1:1039469/69‑1 (MQ=255)
tattaCCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATAaca < 1:82902/69‑1 (MQ=255)
tattaCCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATAac < 1:998434/68‑1 (MQ=255)
gaAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATAACACATCACCTGAt < 1:2696815/69‑1 (MQ=255)
gaAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATAACAAATCACCTGAt < 1:3376418/69‑1 (MQ=255)
aaCTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATAACACATCACCTGATTg < 1:2436670/69‑1 (MQ=255)
aaCTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATAACACATCACCTGATTg < 1:1594939/69‑1 (MQ=255)
aCTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATAACACATCACCTGATTGc < 1:689330/69‑1 (MQ=255)
atttattAATCCTGCGCCACACGCATAATCAGGGAAGATa > 1:2852453/1‑40 (MQ=38)
atttattAATCCTGCGCCACACGCATAATCAGGGAAGATa > 1:2711847/1‑40 (MQ=38)
atttattAATCCTGCGCCACACGCATAATCAGGGAAGATa > 1:2717500/1‑40 (MQ=38)
atttattAATCCTGCGCCACACGCATAATCAGGGAAGATa > 1:283959/1‑40 (MQ=38)
atttattAATCCTGCGCCACACGCATAATCAGGGAAGATa > 1:147317/1‑40 (MQ=38)
atttattAATCCTGCGCCACACGCATAATCAGGGAAGATa > 1:25040/1‑40 (MQ=38)
atttattAATCCTGCGCCACACGCATAATCAGGGAAGATa > 1:1603720/1‑40 (MQ=38)
atttattAATCCTGCGCCACACGCATAATCAGGGAAGATa > 1:936491/1‑40 (MQ=38)
atttattAATCCTGCGCCACACGCATAATCAGGGAAGATa > 1:1531572/1‑40 (MQ=38)
atttattAATCCTGCGACACACGCATAATCAGGGAAGATa > 1:340637/1‑40 (MQ=37)
tattaATCCTGCGCCACACGCATAACCAGAGAAGAt > 1:367791/1‑36 (MQ=255)
tattaATCCTGCGCCACACGCATAACCAGAGAAGAt > 1:2709083/1‑36 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:3209105/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:578528/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:3419352/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:3338172/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:1407325/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:1467519/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:773754/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:2458242/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:1102490/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:2227427/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:1747141/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:2195027/69‑1 (MQ=255)
cacaCGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:2057622/69‑1 (MQ=255)
cacaCGAATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGTTAttt < 1:3054152/69‑1 (MQ=255)
actcGCATAATGAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:1229359/65‑1 (MQ=255)
acacGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:648645/68‑1 (MQ=255)
acacGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:986891/68‑1 (MQ=255)
acacGCATAATCAGGGAAGATAACACATCACCTGAATTCACTGAGTTATCTGTCAGTTTCAGGTAttt < 1:1380428/68‑1 (MQ=255)
aTAACCAGAGAATATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTa < 1:3185621/69‑1 (MQ=255)
aTAACCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTa < 1:1893926/69‑1 (MQ=255)
aTAACCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTa < 1:2589442/69‑1 (MQ=255)
aTAACCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTa < 1:2439852/69‑1 (MQ=255)
aTAACCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTa < 1:841661/69‑1 (MQ=255)
aTAACCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTa < 1:845640/69‑1 (MQ=255)
aTAACCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTa < 1:2311701/69‑1 (MQ=255)
aTAACCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTa < 1:2006939/69‑1 (MQ=255)
tAACCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCa > 1:2408352/1‑54 (MQ=255)
aCCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTaaa > 1:804097/1‑68 (MQ=255)
aCCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTaaa > 1:1012972/1‑68 (MQ=255)
|
TGTTTATTACCTGGAGAAACTTACAATTTTATTTATTAATCCTGCGCCACACGCATAACCAGAGAAGATAACACATCACCTGATTGCACTGAGTTATCTGTCAGTTTCAGGTATTTTGCTTTAAA > minE/1359856‑1359980
|
| 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
