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 |
312,246 |
C→T |
57.0% |
A209A (GCG→GCA) |
acrB ← |
multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 312,246 | 0 | C | T | 57.0%
| 18.5
/ 61.0
| 79 | A209A (GCG→GCA) | acrB | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base C (23/11); new base T (10/35); total (33/46) |
| Fisher's exact test for biased strand distribution p-value = 7.37e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAGCTGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGTT > minE/312183‑312293
|
aaGCTGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTTACCCGCCGCAACCTGGGCGTTCTGCGCttt < 1:809402/69‑1 (MQ=255)
aaGCTGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCACCCTGGGCGTTCTGCGCttt > 1:1705023/1‑69 (MQ=255)
aaGCTGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCttt < 1:2277039/69‑1 (MQ=255)
aaGCTGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCttt > 1:2232589/1‑69 (MQ=255)
aaGCTGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCttt < 1:2255684/69‑1 (MQ=255)
aaGCTGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCttt > 1:1302374/1‑69 (MQ=255)
tGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATg > 1:3118144/1‑69 (MQ=255)
tGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATg > 1:600790/1‑69 (MQ=255)
tGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATg > 1:3252444/1‑69 (MQ=255)
tGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATg > 1:1897063/1‑69 (MQ=255)
gCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGt > 1:2686746/1‑69 (MQ=255)
gCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGt > 1:3324381/1‑69 (MQ=255)
tttCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAAt > 1:2842782/1‑69 (MQ=255)
aCCGGCGGCGTACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGAc > 1:2452437/1‑68 (MQ=255)
aCCGGCGGCGTACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGAc > 1:2105950/1‑68 (MQ=255)
aCCGGCGGCGTACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGAc > 1:3344012/1‑68 (MQ=255)
aCCGGCGGCGTACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGAc > 1:676711/1‑68 (MQ=255)
aCCGGCGGCGTACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGAc > 1:1844992/1‑68 (MQ=255)
aCCGGCGGCGTACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGAc > 1:1816651/1‑68 (MQ=255)
aCCGGCGGCGTACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGAc > 1:1694619/1‑68 (MQ=255)
aCCGGCGGCGTACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGAc > 1:1248518/1‑68 (MQ=255)
aCCGGCGGCGTACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGAc > 1:696110/1‑68 (MQ=255)
aCCGGCGGCGTACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGAc > 1:889310/1‑68 (MQ=255)
ggcggcGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCa > 1:1422177/1‑69 (MQ=255)
ggcggcGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCa > 1:2179174/1‑69 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:101998/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:3185091/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:2941744/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:1410470/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:2375443/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:145919/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:1478262/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:863649/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:2112361/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:1957006/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:603127/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:2178183/53‑1 (MQ=255)
tACCACCGAGCTGACCAGCTGCAACCTGAGCGTTCTGTGCTTTGATGGCGGTa < 1:1604366/53‑1 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGt < 1:1736255/50‑1 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGt < 1:1647967/50‑1 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGt < 1:3017226/50‑1 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGt < 1:2763983/50‑1 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGt < 1:3425509/50‑1 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTaa > 1:3361060/1‑52 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGtt > 1:2531617/1‑69 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGtt > 1:366514/1‑69 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGtt > 1:1992864/1‑69 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGtt > 1:3324596/1‑69 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGtt > 1:89342/1‑69 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGtt > 1:3138870/1‑69 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGtt > 1:216625/1‑69 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGtt > 1:1114657/1‑69 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGt > 1:1848539/1‑68 (MQ=255)
ccaccGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGt > 1:1507303/1‑68 (MQ=255)
ccgccgCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGt < 1:3401244/69‑1 (MQ=255)
ccgccgCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGt < 1:1071213/69‑1 (MQ=255)
ccgccgCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGt < 1:455265/69‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:2014678/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:949365/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:91304/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:910123/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:1236630/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:1324962/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:1554093/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:1623018/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:730190/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:164367/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:3312114/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:2027481/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:218778/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:565035/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:2306883/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:2502872/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:2592171/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:2659053/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:2756571/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:2942323/65‑1 (MQ=255)
gcAACCTGAGCGTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:3051038/65‑1 (MQ=255)
gTTCTGTGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGtt < 1:701866/54‑1 (MQ=255)
|
AAGCTGTTGGCCTTTCACCGGCGGCGTACCACCGAGCTGACCCGCCGCAACCTGGGCGTTCTGCGCTTTGATGGCGGTAATGACATCAACCGGCGTTAGCTGGAATTTGTT > minE/312183‑312293
|
| 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
