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 |
728,538 |
T→C |
38.8% |
I175I (ATT→ATC) |
fabH → |
3‑oxoacyl‑[acyl‑carrier‑protein] synthase III |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 728,538 | 0 | T | C | 38.8%
| 23.5
/ 34.0
| 54 | I175I (ATT→ATC) | fabH | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase III |
| Reads supporting (aligned to +/- strand): ref base T (23/10); new base C (12/9); total (35/19) |
| Fisher's exact test for biased strand distribution p-value = 3.92e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.58e-01 |
TTATTATTTTTGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGC > minE/728474‑728601
|
ttattattTTTGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTcc > 1:742991/1‑68 (MQ=255)
ttattattTTTGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCa > 1:2166463/1‑69 (MQ=255)
ttattattTTTGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCa > 1:556565/1‑69 (MQ=255)
ttattattTTTGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCa > 1:2649329/1‑69 (MQ=255)
ttattattTTTGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCa > 1:758510/1‑69 (MQ=255)
ttattattTTTGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCa > 1:1432661/1‑69 (MQ=255)
ttattattTTTGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCa > 1:1459274/1‑69 (MQ=255)
tttGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTg < 1:864884/69‑1 (MQ=255)
tttGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTg < 1:2570620/69‑1 (MQ=255)
tttGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTg < 1:1754566/69‑1 (MQ=255)
gcgcGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTc < 1:817722/49‑1 (MQ=255)
gcgcGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTc < 1:125549/49‑1 (MQ=255)
ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt > 1:409819/1‑69 (MQ=255)
ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt > 1:1358730/1‑69 (MQ=255)
ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt > 1:719249/1‑69 (MQ=255)
ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt > 1:2782660/1‑69 (MQ=255)
ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt < 1:1845060/69‑1 (MQ=255)
ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt < 1:854847/69‑1 (MQ=255)
ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt > 1:1947116/1‑69 (MQ=255)
ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt > 1:3237160/1‑69 (MQ=255)
ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt > 1:3074882/1‑69 (MQ=255)
gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa < 1:3037171/68‑1 (MQ=255)
gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa < 1:2464329/68‑1 (MQ=255)
gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa < 1:636226/68‑1 (MQ=255)
gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa < 1:681261/68‑1 (MQ=255)
gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa < 1:69192/68‑1 (MQ=255)
gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa < 1:1395079/68‑1 (MQ=255)
gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa < 1:831251/68‑1 (MQ=255)
gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa < 1:1083011/68‑1 (MQ=255)
gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa < 1:972348/68‑1 (MQ=255)
gctggctgCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTg < 1:106420/65‑1 (MQ=255)
gctggctgCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTg < 1:1933741/65‑1 (MQ=255)
gctggctgCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTg < 1:1937794/65‑1 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACgg > 1:984112/1‑53 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACgg > 1:1163992/1‑53 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACgg > 1:1169042/1‑53 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACgg > 1:1675348/1‑53 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACgg > 1:908999/1‑53 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACgg > 1:2510334/1‑53 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACgg > 1:3404366/1‑53 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACgg > 1:3374742/1‑53 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACgg > 1:2797590/1‑53 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACgg > 1:3118973/1‑53 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACg > 1:1319930/1‑52 (MQ=255)
ctggctgCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCAAGCCGACg > 1:890712/1‑52 (MQ=255)
gAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCt > 1:423717/1‑59 (MQ=255)
gAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCt > 1:2668413/1‑59 (MQ=255)
gAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCt > 1:1687263/1‑59 (MQ=255)
gAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCt > 1:2958788/1‑59 (MQ=255)
gCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACg > 1:2931415/1‑68 (MQ=255)
atcatcTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa < 1:9380/41‑1 (MQ=255)
aTCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACcgc > 1:1601462/1‑69 (MQ=255)
aTCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACcgc > 1:1708350/1‑69 (MQ=255)
aTCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACcgc > 1:1022597/1‑69 (MQ=255)
aTCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACcgc > 1:201752/1‑69 (MQ=255)
|
TTATTATTTTTGGCGATGGCGCGGGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGC > minE/728474‑728601
|
| 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
