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 |
1,120,174 |
T→C |
25.8% |
K83K (AAA→AAG) |
nlpC ← |
predicted lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,120,174 | 0 | T | C | 25.8%
| 97.0
/ 31.2
| 85 | K83K (AAA→AAG) | nlpC | predicted lipoprotein |
| Reads supporting (aligned to +/- strand): ref base T (42/21); new base C (7/15); total (49/36) |
| Fisher's exact test for biased strand distribution p-value = 5.96e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01 |
CCAGGTCACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCG > minE/1120116‑1120235
|
ccAGGTCACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGCTTGGttt > 1:576295/1‑66 (MQ=255)
ccAGGTCACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGCTTGGTTTCAc > 1:1241659/1‑69 (MQ=255)
ccAGGTCACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGCTTGGTTTCAc > 1:946637/1‑69 (MQ=255)
ccAGGTCACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGCTTGGTTTCAc > 1:2911799/1‑69 (MQ=255)
ccAGGTCACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGCTTGGTTTCAc > 1:269480/1‑69 (MQ=255)
ccAGGTCACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGCTTGGTTTCAc > 1:1614736/1‑69 (MQ=255)
ccAGGTCACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGCTTGGTTTCAc > 1:1755984/1‑69 (MQ=255)
cAGGTCACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTg < 1:1703900/61‑1 (MQ=255)
cACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCa > 1:955244/1‑69 (MQ=255)
cACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCa > 1:3278402/1‑69 (MQ=255)
cACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCa > 1:3109980/1‑69 (MQ=255)
cACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCa > 1:2943815/1‑69 (MQ=255)
cACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCa > 1:2260811/1‑69 (MQ=255)
aCCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCa > 1:3308855/1‑68 (MQ=255)
aCCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAg > 1:576645/1‑69 (MQ=255)
aCCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAg > 1:3332199/1‑69 (MQ=255)
aCCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAg > 1:30512/1‑69 (MQ=255)
aCCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAg > 1:2039507/1‑69 (MQ=255)
aCCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAg > 1:2984619/1‑69 (MQ=255)
aCCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAg > 1:2535727/1‑69 (MQ=255)
aCCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAg > 1:1376133/1‑69 (MQ=255)
aCCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAg > 1:808270/1‑69 (MQ=255)
aCCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAg > 1:2727386/1‑69 (MQ=255)
aCCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAg > 1:2716610/1‑69 (MQ=255)
tCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTgg > 1:3134606/1‑43 (MQ=255)
tCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGaa > 1:3161844/1‑68 (MQ=255)
tCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGaa > 1:71692/1‑68 (MQ=255)
tCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGaa > 1:65451/1‑68 (MQ=255)
tCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGaa > 1:379759/1‑68 (MQ=255)
cGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTgg < 1:2592670/42‑1 (MQ=255)
tttATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCATCTGCAAATCGAAACGATc > 1:2109150/1‑69 (MQ=255)
tttATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGc > 1:2301824/1‑55 (MQ=255)
tttATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGa > 1:240039/1‑67 (MQ=255)
tttATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATc > 1:3430060/1‑69 (MQ=255)
tttATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATc > 1:2827275/1‑69 (MQ=255)
tttATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATc > 1:2881983/1‑69 (MQ=255)
tttATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATc > 1:2936500/1‑69 (MQ=255)
tttATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATc > 1:2595103/1‑69 (MQ=255)
tttATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATc > 1:1755618/1‑69 (MQ=255)
tttATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATc > 1:552599/1‑69 (MQ=255)
tttATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATc > 1:79673/1‑69 (MQ=255)
tGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGt > 1:1292963/1‑68 (MQ=255)
tGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGt > 1:2221751/1‑68 (MQ=255)
tGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGt > 1:2101173/1‑68 (MQ=255)
tGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGt > 1:287732/1‑68 (MQ=255)
gTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTcac < 1:2479462/68‑1 (MQ=255)
gTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTcac < 1:444755/68‑1 (MQ=255)
gTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTcac < 1:2171379/68‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACCACcaca < 1:440187/69‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:2866882/69‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:2184268/69‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:1169489/69‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:3423134/69‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:2209195/69‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:2043655/69‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:2477931/69‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:762055/69‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:3155538/69‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:1650601/69‑1 (MQ=255)
aTAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:3268143/69‑1 (MQ=255)
agagGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGaa < 1:3268462/42‑1 (MQ=255)
agagGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGaa < 1:2597166/42‑1 (MQ=255)
agagGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGaa < 1:1289271/42‑1 (MQ=255)
agagGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGaa < 1:3379588/42‑1 (MQ=255)
agagGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACaaa > 1:2717992/1‑69 (MQ=255)
agagGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACaa > 1:2825846/1‑68 (MQ=255)
gagGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAGACGATCGCGCATCGTCACAACCACAAAt > 1:1522093/1‑69 (MQ=255)
gagGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAAt > 1:2689063/1‑69 (MQ=255)
gagGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAAt > 1:75713/1‑69 (MQ=255)
gagGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGAGCATCGTCACAACCACAAAt > 1:1635829/1‑69 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:3185370/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:1523383/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:780148/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:1633768/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:1660768/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:640347/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:599827/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:1687949/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:1771610/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:2014354/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:2071432/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:2276970/69‑1 (MQ=255)
cTTGTTGCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCAACGTCACAACCACAAATCCCg < 1:3328631/69‑1 (MQ=255)
ttgttgCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:1024045/68‑1 (MQ=255)
ttgttgCTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:2791814/68‑1 (MQ=255)
tgttgtTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACcaca < 1:1054107/60‑1 (MQ=255)
tgttgcTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCg < 1:1268983/67‑1 (MQ=255)
|
CCAGGTCACCTGGCAGCAACTCGTCTTTATCAATTTGCGTGCCAATAGAGGCTTGTTGTTTGGTTTCACGGGGCAGCTGCAAATCGAAACGATCGCGCATCGTCACAACCACAAATCCCG > minE/1120116‑1120235
|
| 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
