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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
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 | 96.8%
| 96.9
/ ‑4.4
| 31 | R527C (CGT→TGT) | cyoB | cytochrome o ubiquinol oxidase subunit I |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (17/13); total (17/14) |
| Fisher's exact test for biased strand distribution p-value = 4.52e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.95e-01 |
ACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTG > NZ_CP009273/444437‑444593
|
aCGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTgg > 1:118653/1‑90 (MQ=255)
taGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGa < 2:304136/90‑1 (MQ=255)
cGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGa > 1:185650/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaa > 1:136908/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaa > 2:510263/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaa > 2:321615/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGTTGCCCACTCCAGCGGACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaa > 2:99511/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGGTGCCCACTCCAGCGGACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGGTCTGGTCGCGGTCGCGAATAGaa > 1:224280/1‑90 (MQ=255)
gAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaaa > 1:560956/1‑90 (MQ=255)
gAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaaa > 1:242190/1‑90 (MQ=255)
tGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAAc > 1:277041/1‑90 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa > 2:71972/1‑90 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa < 2:560956/90‑1 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa < 1:383177/90‑1 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa < 2:442395/90‑1 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa < 2:242190/90‑1 (MQ=255)
cGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATAccc > 1:44859/1‑90 (MQ=255)
cGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATAccc > 2:355453/1‑90 (MQ=255)
cACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAgcg < 1:62268/90‑1 (MQ=255)
cACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAgcg < 1:298431/90‑1 (MQ=255)
cACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAgcg > 2:226512/1‑90 (MQ=255)
cccACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCaa < 1:510263/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 2:144458/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 2:466122/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 2:486071/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 1:431624/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 1:358857/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 1:321615/90‑1 (MQ=255)
cGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTg > 1:260323/1‑90 (MQ=255)
cGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTg > 1:574971/1‑90 (MQ=255)
cGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTg > 1:218254/1‑90 (MQ=255)
|
ACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTG > NZ_CP009273/444437‑444593
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 25 ≤ 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
GTGCGGCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCATCAGC > NZ_CP009273/444427‑444616
|
GTGCGGCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGG > SRR3722109.120123/1‑100 (MQ=60)
GTGCGGCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGG < SRR3722109.540895/100‑1 (MQ=60)
AGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGA > SRR3722109.187935/1‑100 (MQ=60)
GTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAA > SRR3722109.138598/1‑100 (MQ=60)
GTGATAGAACGGAGGCGGGGAAGAGGGTGCCCACTCCAGCGGACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGGTCTGGTCGCGGTCGCGAATAGAA > SRR3722109.226951/1‑100 (MQ=60)
TTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAA > SRR3722109.569466/1‑100 (MQ=60)
TTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAA > SRR3722109.245039/1‑100 (MQ=60)
GGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAAC > SRR3722109.280529/1‑100 (MQ=60)
CTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCC > SRR3722109.45392/1‑100 (MQ=60)
CTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCC < SRR3722109.388636/100‑1 (MQ=60)
CACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTAC < SRR3722109.63007/100‑1 (MQ=60)
CACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTAC < SRR3722109.302289/100‑1 (MQ=60)
CCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTG > SRR3722109.263488/1‑100 (MQ=60)
CCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTG > SRR3722109.220875/1‑100 (MQ=60)
CCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTG > SRR3722109.583693/1‑100 (MQ=60)
CCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGC < SRR3722109.517986/100‑1 (MQ=60)
CACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCAC < SRR3722109.363800/100‑1 (MQ=60)
CACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCAC < SRR3722109.325863/100‑1 (MQ=60)
CACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCAC < SRR3722109.437987/100‑1 (MQ=60)
GGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCAT > SRR3722109.186357/1‑100 (MQ=60)
ACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCATCAGC < SRR3722109.487498/100‑1 (MQ=60)
|
GTGCGGCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCATCAGC > NZ_CP009273/444427‑444616
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
