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 |
|
A1 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,157,782 |
T→C |
88.3% |
L128S (TTG→TCG) |
mdtB → |
multidrug efflux system, subunit B |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,157,782 | 0 | T | C | 88.3%
| 171.7
/ 11.7
| 60 | L128S (TTG→TCG) | mdtB | multidrug efflux system, subunit B |
| Reads supporting (aligned to +/- strand): ref base T (2/5); new base C (19/34); total (21/39) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.06e-01 |
AACATTACCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTTGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGATCATGA > W3110S.gb/2157717‑2157847
|
aaCATTACCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACttgttg > 1:832310/1‑67 (MQ=255)
aaCATTACCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACttgttg > 1:1212912/1‑67 (MQ=255)
ttACCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCg > 1:2122896/1‑66 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGGAGTGCAGGGCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCg < 1:2704938/68‑1 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTTGCCGAGCGa < 1:380578/69‑1 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTTGCCGAGCGa < 1:2299969/69‑1 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCg < 1:2899314/68‑1 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCg < 1:2399863/68‑1 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGa < 1:2889397/69‑1 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGa < 1:2783799/69‑1 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGa < 1:3052264/69‑1 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGa < 1:2520234/69‑1 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGa > 1:3603214/1‑69 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGa < 1:1970383/69‑1 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGa > 1:1866528/1‑69 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGa < 1:586612/69‑1 (MQ=255)
aCCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGa < 1:889806/69‑1 (MQ=255)
cTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTg > 1:3585056/1‑69 (MQ=255)
tggcGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTa < 1:2970924/65‑1 (MQ=255)
tGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTa < 1:41577/68‑1 (MQ=255)
tGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTa < 1:1486383/68‑1 (MQ=255)
tGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTa < 1:1338709/68‑1 (MQ=255)
gTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAAc > 1:435364/1‑69 (MQ=255)
gTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAAc > 1:2652996/1‑69 (MQ=255)
gTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAAc > 1:2789907/1‑69 (MQ=255)
gTCGCCGAGCAGGAAGTGCAGGCAGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAAc > 1:274761/1‑69 (MQ=255)
tCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTaa < 1:2974405/67‑1 (MQ=255)
tCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTaa < 1:2978703/67‑1 (MQ=255)
tCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTaa < 1:3522249/67‑1 (MQ=255)
gCAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCaa < 1:3022541/69‑1 (MQ=255)
cAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCa > 1:728378/1‑67 (MQ=255)
cAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCa < 1:606176/67‑1 (MQ=255)
cAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCa < 1:3495893/67‑1 (MQ=255)
cAGGCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCa < 1:3285331/67‑1 (MQ=255)
ggCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGt < 1:1972020/69‑1 (MQ=255)
ggCCGCGATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGt < 1:2324519/69‑1 (MQ=255)
cgcgATTAACGCTGCGACCAACTTGTTGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGaa < 1:3335024/69‑1 (MQ=255)
cgcgATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGcc > 1:62642/1‑42 (MQ=255)
cgcgATTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGaa < 1:2987932/69‑1 (MQ=255)
aTTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAAccc > 1:3099295/1‑68 (MQ=255)
aTTAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAAccc > 1:1833428/1‑68 (MQ=255)
ttAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAAccc > 1:3574161/1‑67 (MQ=255)
ttAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAAccc > 1:1993505/1‑67 (MQ=255)
ttAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAAccc > 1:3717664/1‑67 (MQ=255)
tAACGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAAccc > 1:1691519/1‑66 (MQ=255)
aCGCTGCGACCAACTTGTCTCCGAGCGATCTGCCTAAcc > 1:1596072/1‑39 (MQ=38)
aCGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGa > 1:324914/1‑60 (MQ=255)
aCGCTGCGACCAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGa > 1:3692472/1‑60 (MQ=255)
aCCAACTTGTTGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATccgccg > 1:1412484/1‑69 (MQ=255)
aCCAACTTGTTGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATccgccg > 1:1518981/1‑69 (MQ=255)
cAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGAt < 1:3247254/69‑1 (MQ=255)
cAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGAt < 1:2660922/69‑1 (MQ=255)
cAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGAt < 1:490655/69‑1 (MQ=255)
cAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGAt < 1:3109686/69‑1 (MQ=255)
cAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGAt < 1:3499323/69‑1 (MQ=255)
cAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGAt < 1:3159390/69‑1 (MQ=255)
cAACTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGAt < 1:3217509/69‑1 (MQ=255)
aCTTGTTGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGAt < 1:2595057/67‑1 (MQ=255)
aCTTGTTGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGAt < 1:1219644/67‑1 (MQ=255)
cTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGATCAt < 1:395442/69‑1 (MQ=255)
cTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGATCAt < 1:573528/69‑1 (MQ=255)
cTTGTCGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGATCAt < 1:750759/69‑1 (MQ=255)
ttgtcgCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGACCCGCCGATCATg < 1:2809438/69‑1 (MQ=255)
tgttgCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGATCATGa > 1:369772/1‑69 (MQ=255)
|
AACATTACCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTTGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGATCATGA > W3110S.gb/2157717‑2157847
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
