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 |
|
A6 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
309,859 |
G→A |
26.7% |
T1005I (ACC→ATC) |
acrB ← |
multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 309,859 | 0 | G | A | 26.7%
| 112.4
/ 42.9
| 71 | T1005I (ACC→ATC) | acrB | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base G (29/23); new base A (8/11); total (37/34) |
| Fisher's exact test for biased strand distribution p-value = 4.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01 |
CACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGCCGAGGATAAA > minE/309792‑309929
|
cacaAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAc > 1:4126667/1‑71 (MQ=255)
acaAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACCCCGGTAcc > 1:5554540/1‑71 (MQ=255)
aaGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTa > 1:5162098/1‑70 (MQ=255)
aaGAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATAccca > 1:849491/1‑68 (MQ=12)
aGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAcc < 1:847248/67‑1 (MQ=255)
aGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAcc < 1:625993/67‑1 (MQ=255)
aGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTAcc < 1:182003/67‑1 (MQ=255)
gAACACCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCAcag > 1:2923753/1‑69 (MQ=255)
acaCCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCg > 1:3298615/3‑71 (MQ=255)
acaCCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCg > 1:4712527/3‑71 (MQ=255)
tACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTa > 1:5670355/1‑65 (MQ=255)
tACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTa > 1:2475731/1‑65 (MQ=255)
aCCGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt < 1:5275557/71‑1 (MQ=255)
cGGTACGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATAccca > 1:5372972/1‑60 (MQ=255)
ggAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTg > 1:309971/1‑71 (MQ=255)
ggAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTg < 1:2365160/71‑1 (MQ=255)
gtaCGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgc < 1:2910880/69‑1 (MQ=255)
gtaCGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgc < 1:2736173/69‑1 (MQ=255)
gAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgc < 1:2729606/71‑1 (MQ=255)
aCGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgc > 1:2623255/1‑71 (MQ=255)
cGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgcg > 1:2352911/1‑71 (MQ=255)
cGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt > 1:487488/1‑64 (MQ=255)
cGAAGAAGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt > 1:1336105/1‑64 (MQ=255)
gaagaaGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTgcgcgc < 1:4858816/71‑1 (MQ=255)
gaagaaGATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgcgcgc < 1:1760126/71‑1 (MQ=12)
aagaagATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt < 1:4603109/62‑1 (MQ=255)
aagaagATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt < 1:1588986/62‑1 (MQ=255)
aagaagATTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGtt < 1:2606199/62‑1 (MQ=255)
gaagaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCgg < 1:1517037/71‑1 (MQ=255)
gaagaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCgg < 1:1306413/71‑1 (MQ=255)
aagaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCATTCTTCGCGCCGGa < 1:448472/71‑1 (MQ=255)
gaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAAc > 1:3420077/1‑71 (MQ=255)
gaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAAc > 1:3216696/1‑71 (MQ=255)
gaTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAAc < 1:91297/71‑1 (MQ=255)
aTTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAAc < 1:2801117/70‑1 (MQ=255)
aTTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgcgcg < 1:4018313/63‑1 (MQ=255)
aTTGCCAGCAACGTTGCAGAGACCATTCCTCCCATTACCCCGATACCCACAGCGTTCTgcgcg < 1:4069408/63‑1 (MQ=255)
gCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAg > 1:4999943/1‑70 (MQ=255)
tACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAg > 1:1582566/1‑71 (MQ=255)
aCCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAg > 1:5516986/1‑70 (MQ=255)
ccGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTa > 1:2665121/1‑71 (MQ=255)
gTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACt > 1:1012766/1‑71 (MQ=255)
ttGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGGGTTCTGCGCGCCGGAACCAGCACCAGTACt > 1:4175240/1‑70 (MQ=255)
cGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGAt < 1:468344/70‑1 (MQ=255)
gTCACCATCCCGCCCATTACACCGGTACCTACTGCGt < 1:4097617/37‑1 (MQ=255)
gTCACCATCCCGCCCATTACACCGGTACCTACTGCGt < 1:5169313/37‑1 (MQ=255)
gTCACCATCCCGCCCATTACACCGGTACCTACTGCGt < 1:4352798/37‑1 (MQ=255)
gTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATaa < 1:2850347/70‑1 (MQ=255)
tCACCATCCCGCCCATTACACCGGTACCTACTGCg < 1:719907/35‑1 (MQ=255)
aCCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAg < 1:2622107/71‑1 (MQ=255)
cATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAAc > 1:1679130/1‑66 (MQ=255)
tCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGa < 1:1986799/43‑1 (MQ=255)
tCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTg > 1:2983748/1‑59 (MQ=255)
tCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCgg > 1:2489622/1‑70 (MQ=255)
ccGCCCATTACACCGGTACCTACTGCGTTCTgcgc > 1:4285740/1‑35 (MQ=255)
ccGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCa > 1:2221300/1‑70 (MQ=255)
cGCCCATTACACCGGTACCTACTGCGTTCTGCGGGCCGGAACCAGCAcc < 1:1454465/49‑1 (MQ=255)
gCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAg > 1:4182180/1‑44 (MQ=255)
gCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAg > 1:1062951/1‑44 (MQ=255)
ccATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACg > 1:3367986/1‑71 (MQ=255)
aTTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGcc < 1:5062096/71‑1 (MQ=255)
aTTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGcc < 1:4369787/71‑1 (MQ=255)
ttACCCCGATACCCACAGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGcc > 1:2923481/1‑70 (MQ=255)
tACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGcc > 1:2110669/1‑69 (MQ=255)
tACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGcc > 1:2464934/1‑69 (MQ=255)
acacCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGCCGAg > 1:2989727/1‑71 (MQ=255)
ccccGATACCCACAGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAg < 1:4620256/68‑1 (MQ=255)
ccccGATACCCACAGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAg < 1:3655006/68‑1 (MQ=255)
cacCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATaa > 1:3283800/1‑63 (MQ=255)
cGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGCCGAGGATa < 1:5235571/71‑1 (MQ=255)
cGGTACCTACTGCGTTCTCCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGCCGAGGAt > 1:1016418/1‑70 (MQ=255)
ggTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGCCGAGGATaa < 1:4032596/71‑1 (MQ=255)
gTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGCCGAGGATaaa < 1:5169148/71‑1 (MQ=255)
|
CACAAAGAATACCGGAACGAAGAAGATTGCCAGTACCGTTGCGGTCACCATCCCGCCCATTACACCGGTACCTACTGCGTTCTGCGCGCCGGAACCAGCACCAGTACTGATAACCAGCGGCATAACGCCGAGGATAAA > minE/309792‑309929
|
| 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
