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 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,225,948 |
G→C |
35.4% |
V129V (GTG→GTC) |
dusB → |
tRNA‑dihydrouridine synthase B |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,225,948 | 0 | G | C | 35.4%
| 61.9
/ 60.4
| 65 | V129V (GTG→GTC) | dusB | tRNA‑dihydrouridine synthase B |
| Reads supporting (aligned to +/- strand): ref base G (14/28); new base C (13/10); total (27/38) |
| Fisher's exact test for biased strand distribution p-value = 1.13e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01 |
ATCGCAAGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGC > minE/2225878‑2226014
|
aTCGCAAGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTg < 1:2765052/71‑1 (MQ=255)
tCGCAAGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGa < 1:2937742/71‑1 (MQ=255)
tCGCAAGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGATCGTGa < 1:1647794/71‑1 (MQ=255)
aGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCa < 1:948338/71‑1 (MQ=255)
aGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGc > 1:3080975/1‑70 (MQ=255)
tCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGt < 1:757032/70‑1 (MQ=255)
gCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAg < 1:556689/67‑1 (MQ=255)
ggTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGt < 1:1589534/71‑1 (MQ=255)
gTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGtt < 1:2126159/71‑1 (MQ=255)
tCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTcc > 1:66000/1‑71 (MQ=255)
cAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGa < 1:2659795/54‑1 (MQ=255)
cAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTcc < 1:2438492/70‑1 (MQ=255)
aGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTg > 1:539541/1‑71 (MQ=255)
gCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGt > 1:3585533/1‑71 (MQ=255)
ccTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTa < 1:1962817/71‑1 (MQ=255)
tctTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCt < 1:1703453/65‑1 (MQ=255)
tctTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCt < 1:2599358/65‑1 (MQ=255)
tctTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCt < 1:2136491/65‑1 (MQ=255)
tctTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTAcc > 1:3098236/1‑71 (MQ=255)
gCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCt < 1:267145/69‑1 (MQ=255)
gCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTAccc < 1:332268/68‑1 (MQ=255)
aGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTg > 1:531706/1‑68 (MQ=255)
aGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTg > 1:3399134/1‑68 (MQ=255)
aGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAg < 1:803908/71‑1 (MQ=255)
tACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTg < 1:663276/39‑1 (MQ=255)
tACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTg < 1:1342520/39‑1 (MQ=255)
tACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTg < 1:3871943/39‑1 (MQ=255)
tACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGAt < 1:1847290/71‑1 (MQ=255)
cccGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGtt < 1:585357/58‑1 (MQ=255)
cccGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGtt < 1:892615/58‑1 (MQ=255)
cccGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCaa > 1:1816980/1‑39 (MQ=255)
ggATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGAt > 1:1588697/1‑66 (MQ=255)
ggATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCa > 1:954311/1‑71 (MQ=255)
ggATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:1363446/1‑45 (MQ=255)
tGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCg < 1:605177/71‑1 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGAc < 1:1373619/39‑1 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTg > 1:348164/1‑71 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGtt > 1:3704622/1‑48 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGtt < 1:3094945/48‑1 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGc < 1:2675007/63‑1 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCt < 1:512169/70‑1 (MQ=255)
tAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTggg > 1:8233/1‑71 (MQ=255)
aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCg > 1:975226/1‑59 (MQ=255)
aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCg > 1:2842529/1‑59 (MQ=255)
aaaTCGATCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCa > 1:2077529/1‑61 (MQ=255)
aaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCa < 1:653931/71‑1 (MQ=255)
aaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCa < 1:3246881/71‑1 (MQ=255)
aTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGAt < 1:796131/54‑1 (MQ=255)
aTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCAc > 1:2851843/1‑71 (MQ=255)
aTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCAc < 1:1517485/71‑1 (MQ=255)
tCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGa > 1:3665451/1‑49 (MQ=255)
cGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCg > 1:1114732/1‑71 (MQ=255)
ccTTTCCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGc < 1:1454119/52‑1 (MQ=255)
cTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAaca < 1:2999846/71‑1 (MQ=255)
cTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAaca < 1:3751180/71‑1 (MQ=255)
cTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAaca < 1:283619/71‑1 (MQ=255)
cTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAac < 1:2556534/70‑1 (MQ=255)
cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAac > 1:1691398/1‑70 (MQ=255)
cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAac < 1:500460/70‑1 (MQ=255)
tACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACGGGAacac > 1:1176048/1‑70 (MQ=255)
tACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACAcc > 1:1521384/1‑71 (MQ=255)
tACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACAcc > 1:3599714/1‑71 (MQ=255)
aCCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCa < 1:538237/60‑1 (MQ=255)
aCCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGTAACACCg > 1:846726/1‑71 (MQ=255)
aCCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCg > 1:656568/1‑71 (MQ=255)
ccGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGaa > 1:2851073/1‑40 (MQ=255)
gAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTaa < 1:2380337/71‑1 (MQ=255)
gAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTaa < 1:2283595/71‑1 (MQ=255)
tCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCTCCGGAACACCGTAACTGc < 1:438477/71‑1 (MQ=255)
gAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGaa > 1:2500163/1‑55 (MQ=255)
gAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGaa > 1:3245625/1‑55 (MQ=255)
gAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTg > 1:1275156/1‑66 (MQ=255)
|
ATCGCAAGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGTAACTGC > minE/2225878‑2226014
|
| 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
