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 |
|
A1 F2 I197 R1
|
189 |
12.7 |
697584 |
97.1% |
677354 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
444,519 |
G→A |
R527C (CGT→TGT) |
cyoB ← |
cytochrome o ubiquinol oxidase subunit I |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 444,519 | 0 | G | A | 100.0%
| 54.2
/ NA
| 17 | R527C (CGT→TGT) | cyoB | cytochrome o ubiquinol oxidase subunit I |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (11/6); total (11/6) |
TACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTA > NZ_CP009273/444436‑444590
|
tACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTg > 2:299529/1‑90 (MQ=255)
aCGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAg > 1:24289/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGGGAACAGaa > 2:265734/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaa > 2:344257/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaa > 2:18908/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaa > 1:47068/1‑90 (MQ=255)
gCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGt < 1:11500/90‑1 (MQ=255)
agGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGaa > 2:213101/1‑90 (MQ=255)
tGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAAc < 1:75884/90‑1 (MQ=255)
tGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAAc > 1:120218/1‑90 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa < 1:344257/90‑1 (MQ=255)
cGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATAccc > 1:78164/1‑90 (MQ=255)
cGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATAccc > 1:81776/1‑90 (MQ=255)
cACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAgcg < 1:299529/90‑1 (MQ=255)
cACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAAAGTACATCTGAATAACGAGGCAGAGAATACCCAgcg < 1:310981/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 1:213101/90‑1 (MQ=255)
ggTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTa > 2:194569/1‑90 (MQ=255)
|
TACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTA > NZ_CP009273/444436‑444590
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGTGAACGTGCGGCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCATCAGCAT > NZ_CP009273/444420‑444618
|
CGTGAACGTGCGGCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACA > SRR3722076.35437/1‑100 (MQ=60)
TGAACGTGCGGCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGT < SRR3722076.47091/100‑1 (MQ=60)
AAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAG > SRR3722076.24580/1‑100 (MQ=60)
GTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAA > SRR3722076.47646/1‑100 (MQ=60)
GCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAAT < SRR3722076.11631/100‑1 (MQ=60)
GGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAAC > SRR3722076.121643/1‑100 (MQ=60)
TGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGA < SRR3722076.76835/100‑1 (MQ=60)
ccatcgtcggcagcgtcagatgtgtataagagaCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCC < SRR3722076.290579/67‑1 (MQ=60)
CTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCC < SRR3722076.349504/100‑1 (MQ=60)
CTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCC > SRR3722076.79140/1‑100 (MQ=60)
CTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCC > SRR3722076.82802/1‑100 (MQ=60)
CACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTAC < SRR3722076.304016/100‑1 (MQ=60)
CACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAAAGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTAC < SRR3722076.315687/100‑1 (MQ=60)
CACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCAC < SRR3722076.215922/100‑1 (MQ=60)
GGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCAT > SRR3722076.107730/1‑100 (MQ=60)
AGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCATCAGCAT < SRR3722076.134584/100‑1 (MQ=60)
|
CGTGAACGTGCGGCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCATCAGCAT > NZ_CP009273/444420‑444618
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
