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 |
|
A5 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,659,825 |
C→T |
11.3% |
M193I (ATG→ATA) |
wzxE ← |
O‑antigen translocase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,659,825 | 0 | C | T | 11.3%
| 208.9
/ 14.1
| 71 | M193I (ATG→ATA) | wzxE | O‑antigen translocase |
| Reads supporting (aligned to +/- strand): ref base C (27/36); new base T (4/4); total (31/40) |
| Fisher's exact test for biased strand distribution p-value = 7.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.48e-01 |
CTGCCCTGCCAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAACC > W3110S.gb/3659756‑3659893
|
ctgccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACa > 1:3763992/1‑71 (MQ=255)
tgccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAAc > 1:1449679/1‑69 (MQ=255)
tgccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat > 1:2282685/1‑71 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACatga < 1:3461025/71‑1 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACatg < 1:780806/70‑1 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat < 1:3428840/69‑1 (MQ=255)
ctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatgatg > 1:3100792/1‑71 (MQ=255)
ctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat < 1:514712/67‑1 (MQ=255)
tgtcAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATgg > 1:478103/4‑71 (MQ=255)
tgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATgg > 1:4148938/1‑71 (MQ=255)
aCCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAg > 1:538421/1‑71 (MQ=255)
ccGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAgg < 1:1367268/71‑1 (MQ=255)
ccGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAgg < 1:4361151/71‑1 (MQ=255)
ccGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAg > 1:3975779/1‑70 (MQ=255)
ccGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATCATGGCGGCAgg < 1:55552/71‑1 (MQ=255)
ttATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAAt < 1:402325/71‑1 (MQ=255)
aTCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAAc > 1:859798/1‑52 (MQ=255)
ccAGCTGGGTTTCAGATAGCTTAAAGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTacca < 1:1616171/71‑1 (MQ=255)
cAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTaccac < 1:1237547/71‑1 (MQ=255)
aGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTaccac > 1:2085712/1‑70 (MQ=255)
aGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTacca > 1:160767/1‑69 (MQ=255)
aGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTa > 1:2909941/1‑66 (MQ=255)
aGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTa > 1:2915140/1‑66 (MQ=255)
cTGGGTTTCAGATAGCTTAACGGGACGACACCACGTTTGATCAAc < 1:1352693/45‑1 (MQ=255)
tGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAAtt < 1:4403947/62‑1 (MQ=255)
tGGGGTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAAtt < 1:4224736/62‑1 (MQ=255)
ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAAc > 1:532018/1‑42 (MQ=255)
ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat < 1:1691684/44‑1 (MQ=255)
ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat < 1:313745/44‑1 (MQ=255)
ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcgc > 1:3343865/1‑71 (MQ=255)
ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcgc < 1:976262/71‑1 (MQ=255)
ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcgc > 1:3094004/1‑71 (MQ=255)
ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcgc < 1:1225733/71‑1 (MQ=255)
ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcgc < 1:155451/71‑1 (MQ=255)
ggTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcg < 1:2848483/70‑1 (MQ=255)
tttCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCTgcg < 1:2762990/68‑1 (MQ=255)
tCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatga > 1:1193365/1‑42 (MQ=255)
tCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCggg < 1:1749249/70‑1 (MQ=255)
cAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGa < 1:3402230/70‑1 (MQ=255)
aGATAGCTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGaa < 1:2012363/70‑1 (MQ=255)
aTAGCTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAAt > 1:2407272/1‑69 (MQ=255)
aTAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTaccac > 1:3951702/1‑57 (MQ=255)
tAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAgt < 1:3683504/47‑2 (MQ=255)
aGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgc > 1:1037756/1‑71 (MQ=255)
gCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgc < 1:2016163/70‑1 (MQ=255)
ttAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAg < 1:4483951/42‑1 (MQ=255)
ttAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAg < 1:4478682/42‑1 (MQ=255)
ttAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgcg < 1:66852/69‑1 (MQ=255)
tAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAAt > 1:1456424/1‑45 (MQ=255)
tAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgcgc > 1:3483590/1‑69 (MQ=255)
aaCGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCa > 1:1917721/1‑64 (MQ=255)
aaCGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCTCCa < 1:1584959/70‑1 (MQ=255)
aCGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAAt < 1:4153643/61‑1 (MQ=255)
cGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTAccacca < 1:106959/50‑1 (MQ=255)
gggATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGAcc > 1:4258975/1‑71 (MQ=255)
gATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAg > 1:3075216/1‑48 (MQ=255)
aTGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAg < 1:3242351/71‑1 (MQ=255)
aTGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAg < 1:3435578/71‑1 (MQ=255)
gACACCACGTTTGATCAATATGATGGCGGCAGGAATTaccac < 1:2441522/42‑1 (MQ=255)
caccacGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGa < 1:3514373/50‑1 (MQ=255)
accacGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCggg < 1:3752572/48‑1 (MQ=255)
accacGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCa > 1:3224287/1‑59 (MQ=255)
ccacGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAAt > 1:4072058/1‑50 (MQ=255)
cacGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGcc > 1:4524795/1‑71 (MQ=255)
cGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGaa > 1:1527505/1‑46 (MQ=255)
cGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGcccc < 1:4493628/71‑1 (MQ=255)
tttGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCt > 1:3127393/1‑70 (MQ=255)
tGATCAACATGATGGCGGCAGGAATTACCACCAGCGCggg > 1:4502530/1‑40 (MQ=255)
atgaaCATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATa < 1:1464346/68‑1 (MQ=255)
aTCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCAt < 1:1850890/70‑1 (MQ=255)
aTCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCAt > 1:2147701/1‑70 (MQ=255)
tCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCa > 1:3937717/1‑48 (MQ=255)
cAACATGATGGCGGCAGGAATTACCACCAGCGCGGGTATc < 1:3046934/40‑1 (MQ=255)
cAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAAc > 1:2824385/1‑71 (MQ=255)
aaCATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAAcc < 1:1829541/71‑1 (MQ=255)
|
CTGCCCTGCCAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAACC > W3110S.gb/3659756‑3659893
|
| 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
