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 |
1,807,019 |
C→T |
60.1% |
G413G (GGC→GGT) |
emrB → |
multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,807,019 | 0 | C | T | 60.1%
| 21.7
/ 35.8
| 55 | G413G (GGC→GGT) | emrB | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base C (3/19); new base T (16/17); total (19/36) |
| Fisher's exact test for biased strand distribution p-value = 9.71e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
GAACGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGT > minE/1806957‑1807083
|
gAACGACTGGCGGCGGCATCGAGCCTCTCTAAC‑TTACGCGAACGCTGGCGGGGTCTATCGGCACGTCg < 1:3178690/68‑1 (MQ=255)
aCGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGAt > 1:250854/1‑69 (MQ=255)
aCGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGAt > 1:2037661/1‑69 (MQ=255)
aCGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGAt > 1:535836/1‑69 (MQ=255)
aCTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAAc < 1:1820569/69‑1 (MQ=255)
cTTTACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTc < 1:1215978/69‑1 (MQ=255)
cTTTACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTc < 1:3225856/69‑1 (MQ=255)
cTTTACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATCTGGACTAACCGCGAGTc < 1:2089580/69‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTGTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:1888811/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTGTCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTc < 1:2692055/68‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:2525767/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:411410/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:460181/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:1312219/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:1699383/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:3136224/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:1459773/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:3045915/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:740045/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:2978917/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:944262/59‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTc < 1:857651/68‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTc < 1:1024930/68‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTc < 1:1656981/68‑1 (MQ=255)
tttACGCGAACGCTGGCGGGGGCTATCGGTACGTCCATAACGACGACGATGTGGACTaa < 1:2701225/59‑1 (MQ=255)
ttACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGa < 1:987755/69‑1 (MQ=255)
ttACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGa < 1:1672084/69‑1 (MQ=255)
ctaaCGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc < 1:3400964/67‑1 (MQ=255)
cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc < 1:2471695/69‑1 (MQ=255)
cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc < 1:24848/69‑1 (MQ=255)
cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc < 1:2727667/69‑1 (MQ=255)
cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc < 1:2770848/69‑1 (MQ=255)
cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc < 1:3321490/69‑1 (MQ=255)
cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc < 1:3000907/69‑1 (MQ=255)
cgAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc < 1:3172098/69‑1 (MQ=255)
gAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCAc < 1:1097507/68‑1 (MQ=255)
aaCGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCa < 1:2053085/69‑1 (MQ=255)
gCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTc < 1:2305795/57‑1 (MQ=255)
gTCTATCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTc < 1:1507087/48‑1 (MQ=25)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGt > 1:1462554/1‑60 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:410887/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:1400453/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:1412986/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:1454930/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:677363/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:54483/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:2046910/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:2034562/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:3280266/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:1685279/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:1688002/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:3021388/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat > 1:3080239/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTAGACCGaat > 1:182287/1‑67 (MQ=255)
tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTAAGTTGACCGaat > 1:1736555/1‑67 (MQ=255)
|
GAACGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGT > minE/1806957‑1807083
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
