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 |
2,947,155 |
T→C |
35.5% |
G37G (GGA→GGG) |
dnaC ← |
DNA biosynthesis protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,947,155 | 0 | T | C | 35.5%
| 41.7
/ 39.1
| 69 | G37G (GGA→GGG) | dnaC | DNA biosynthesis protein |
| Reads supporting (aligned to +/- strand): ref base T (22/22); new base C (11/13); total (34/35) |
| Fisher's exact test for biased strand distribution p-value = 8.03e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.66e-01 |
TAAAGGTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATGGGCAGG > minE/2947094‑2947220
|
tAAAGGTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGtt > 1:1077536/1‑69 (MQ=255)
tAAAGGTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGtt > 1:1392382/1‑69 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:2865145/69‑1 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:1859564/69‑1 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:1993070/69‑1 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:2080813/69‑1 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:2316314/69‑1 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:2681907/69‑1 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:2830550/69‑1 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:37971/69‑1 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:491571/69‑1 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:60447/69‑1 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:935849/69‑1 (MQ=255)
ggTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:1001719/69‑1 (MQ=255)
gcgcTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCttttt > 1:1011021/1‑68 (MQ=255)
gcgcTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCttttt > 1:504746/1‑68 (MQ=255)
gcgcTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCttttt > 1:2632154/1‑68 (MQ=255)
gcgcTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCttttt > 1:720168/1‑68 (MQ=255)
tttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTgccaggccag < 1:2800955/69‑1 (MQ=255)
tttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTgccaggccag < 1:1821482/69‑1 (MQ=255)
tttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTgccaggccag < 1:1036649/69‑1 (MQ=255)
tttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTgccaggccag < 1:689708/69‑1 (MQ=255)
tttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTgccaggccag < 1:58611/69‑1 (MQ=255)
tttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTgccaggccag < 1:2724490/69‑1 (MQ=255)
tttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTgccaggccag < 1:406722/69‑1 (MQ=255)
tttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt < 1:1944945/57‑1 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt > 1:3364292/1‑56 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt > 1:1556312/1‑56 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt > 1:3391223/1‑56 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt > 1:2490412/1‑56 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt > 1:2433025/1‑56 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt > 1:408080/1‑56 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt > 1:230521/1‑56 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt > 1:217012/1‑56 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt > 1:860236/1‑56 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCCCCTTGTTCttt > 1:927901/1‑56 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCACCTTGTTCttt > 1:453416/1‑56 (MQ=255)
ttCATCGCCCGATTTTCACGTTCGAGAGAGGCGGAGCGGATCGCCCCTTGTTCttt > 1:1295997/1‑56 (MQ=255)
aTCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCagtag < 1:400519/68‑1 (MQ=255)
aTCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCagtag < 1:2833879/68‑1 (MQ=255)
gTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTg < 1:1692955/68‑1 (MQ=255)
ttCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGaa < 1:1195134/69‑1 (MQ=255)
ttCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGaa < 1:3110759/69‑1 (MQ=255)
ttCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGaa < 1:197118/69‑1 (MQ=255)
ttCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGaa < 1:2098489/69‑1 (MQ=255)
cGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTg > 1:2363546/1‑65 (MQ=255)
gcggcgGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGt > 1:195121/1‑69 (MQ=255)
gcggcgGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGt > 1:242162/1‑69 (MQ=255)
gcggcgGAGCGGATCGCTCCTTGTTCTTTTTGCCACGCCAGTAGTTCTTCa > 1:1034156/1‑51 (MQ=255)
cggagcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGa < 1:1574751/69‑1 (MQ=255)
cggagcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGa < 1:3400157/69‑1 (MQ=255)
cggagcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGa < 1:3418759/69‑1 (MQ=255)
cggagcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGa < 1:913497/69‑1 (MQ=255)
cggagcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGa < 1:53389/69‑1 (MQ=255)
cggagcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGa < 1:455097/69‑1 (MQ=255)
ggagcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGa < 1:488447/68‑1 (MQ=255)
ggagcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGa < 1:3411696/68‑1 (MQ=255)
gcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGatat > 1:3431699/1‑68 (MQ=255)
gcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATg > 1:1875726/1‑69 (MQ=255)
gcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATg > 1:2170864/1‑69 (MQ=255)
gcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATg > 1:2221510/1‑69 (MQ=255)
gcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATg > 1:2358218/1‑69 (MQ=255)
gcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATg > 1:108903/1‑69 (MQ=255)
gcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATg > 1:717025/1‑69 (MQ=255)
gcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATg > 1:2000570/1‑69 (MQ=255)
gcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATg > 1:1651974/1‑69 (MQ=255)
gcggaTCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATg > 1:1332933/1‑69 (MQ=255)
cGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATGggcagg > 1:1150228/1‑69 (MQ=255)
cGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATGggcagg > 1:1767674/1‑69 (MQ=255)
|
TAAAGGTGCGCTGCATTTTCATCGCCCGATTTTCACGTTCGAGAGCGGCGGAGCGGATCGCTCCTTGTTCTTTTTGCCAGGCCAGTAGTTCTTCACCCGTTTTGAATGCGGGTTTGATATGGGCAGG > minE/2947094‑2947220
|
| 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
