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 |
540,292 |
C→T |
34.6% |
L241L (CTG→CTA) |
rhtA ← |
threonine and homoserine efflux system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 540,292 | 0 | C | T | 34.6%
| 55.4
/ 40.9
| 75 | L241L (CTG→CTA) | rhtA | threonine and homoserine efflux system |
| Reads supporting (aligned to +/- strand): ref base C (28/21); new base T (7/19); total (35/40) |
| Fisher's exact test for biased strand distribution p-value = 1.58e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01 |
GGTGTCAGTGTTTCTCCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCAG > minE/540227‑540354
|
ggTGTCAGTGTTTCTCCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAg < 1:3115819/68‑1 (MQ=255)
ggTGTCAGTGTTTCTCCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAg < 1:221492/68‑1 (MQ=255)
ggTGTCAGTGTTTCTCCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAg < 1:1870139/68‑1 (MQ=255)
ggTGTCAGTGTTTCTCCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAg < 1:2949992/68‑1 (MQ=255)
ggTGTCAGTGTTTCTCCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAg < 1:3144541/68‑1 (MQ=255)
ggTGTCAGTGTTTCTCCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAg < 1:37798/68‑1 (MQ=255)
ggTGTCAGTGTTTCTCCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAg < 1:1164190/68‑1 (MQ=255)
tttCTCCGAGTAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCACCGTACCAAATg > 1:50301/1‑69 (MQ=255)
tttCTCCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATg > 1:1883461/1‑69 (MQ=255)
tttCTCCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATg > 1:897527/1‑69 (MQ=255)
tctcCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCa < 1:3212818/63‑1 (MQ=255)
tctcCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCa < 1:1538746/63‑1 (MQ=255)
tctcCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCa < 1:196703/63‑1 (MQ=255)
tctcCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTc > 1:2319644/1‑69 (MQ=255)
tctcCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTc > 1:3183349/1‑69 (MQ=255)
tctcCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTc > 1:2459946/1‑69 (MQ=255)
tctcCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTc > 1:1624279/1‑69 (MQ=255)
tctcCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTc > 1:2506693/1‑69 (MQ=255)
tctcCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTc > 1:2939354/1‑69 (MQ=255)
tctcCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTc > 1:181514/1‑69 (MQ=255)
tctcCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTc > 1:2201763/1‑69 (MQ=255)
aGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCgt < 1:2233307/66‑1 (MQ=255)
aGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCgt < 1:2612658/66‑1 (MQ=255)
aGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCgt < 1:494685/66‑1 (MQ=255)
aGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCgt < 1:2789573/66‑1 (MQ=255)
aGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCgt < 1:1170412/66‑1 (MQ=255)
aGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCgt < 1:1667450/66‑1 (MQ=255)
aGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCgt < 1:1346343/66‑1 (MQ=255)
aGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCgt < 1:628860/66‑1 (MQ=255)
aGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCgt < 1:1291620/66‑1 (MQ=255)
gCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATc > 1:2566441/1‑69 (MQ=255)
gCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATc > 1:3149018/1‑69 (MQ=255)
gccagcGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCAtt < 1:2250387/69‑1 (MQ=255)
gccagcGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCAtt < 1:1068348/69‑1 (MQ=255)
gccagcGCAGGTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAACCGGGTGAGGGCAATCAtt > 1:2146239/1‑69 (MQ=255)
gccagcGCAGGTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGGAATCAtt > 1:962609/1‑69 (MQ=255)
gccagcGCAGGTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCAtt > 1:2455056/1‑69 (MQ=255)
gccagcGCAGGTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCAtt > 1:1234603/1‑69 (MQ=255)
gccagcGCAGGTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCAtt > 1:1994301/1‑69 (MQ=255)
gccagcGCAGGTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCAtt > 1:1334082/1‑69 (MQ=255)
gccagcGCAGGTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCAtt > 1:1482051/1‑69 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:2072244/67‑1 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:1213776/67‑1 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:751314/67‑1 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:654301/67‑1 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:1287264/67‑1 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:391883/67‑1 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:1426988/67‑1 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:30845/67‑1 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:295168/67‑1 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:211344/67‑1 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:1987834/67‑1 (MQ=255)
caggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:1885912/67‑1 (MQ=255)
aggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:882021/67‑1 (MQ=255)
aggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:2449199/67‑1 (MQ=255)
aggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:57135/67‑1 (MQ=255)
aggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:3312824/67‑1 (MQ=255)
aggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:379833/67‑1 (MQ=255)
aggTTCCATGCTCATTAGCGTACCAAATGTGCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:1977010/67‑1 (MQ=255)
aggTTCCATGCTCATTAGCGTACCAAATGTGCGGGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCg < 1:1400508/67‑1 (MQ=255)
tCCATGCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATaa > 1:108683/1‑69 (MQ=255)
tCCATGCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATaa > 1:2063448/1‑69 (MQ=255)
tCCATGCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATaa > 1:2027307/1‑69 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGTGTGAGGGCAATCATTTCCAGCGAATAAGGCag > 1:718269/1‑69 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCag > 1:430828/1‑69 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCag > 1:3398254/1‑69 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCag > 1:124891/1‑69 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCag > 1:3289984/1‑69 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCag > 1:2802642/1‑69 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCag > 1:1798366/1‑69 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCag > 1:1619604/1‑69 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCag > 1:957155/1‑69 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCag > 1:1775655/1‑69 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCa > 1:1718663/1‑68 (MQ=255)
gCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTACATCGAATAAGGCag > 1:3110876/1‑69 (MQ=255)
|
GGTGTCAGTGTTTCTCCGAGGAAAATCATCCCGGAAACGGCAGCCAGCGCCGGTTCCATGCTCATCAGCGTACCAAATGTCCGTGTTGGCAAACGGGTGAGGGCAATCATTTCCAGCGAATAAGGCAG > minE/540227‑540354
|
| 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
