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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 88.6%
| 91.4
/ 0.5
| 35 | R527C (CGT→TGT) | cyoB | cytochrome o ubiquinol oxidase subunit I |
| Reads supporting (aligned to +/- strand): ref base G (2/2); new base A (14/17); total (16/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01 |
ACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTG > NZ_CP009273/444437‑444593
|
aCGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCGCTCCCGCGTACGGCCACCCCACGGGGCGCCAGCCAGGTCCCAGTTCTgg > 2:680471/1‑90 (MQ=255)
aCGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTgg > 2:668503/1‑90 (MQ=255)
aCGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGCACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTgg > 2:58756/1‑90 (MQ=255)
cGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTggt > 1:829624/1‑90 (MQ=255)
aaaGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTggtcgcg > 1:432601/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaa > 1:224630/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaa > 1:415314/1‑90 (MQ=255)
ggAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGaa > 1:135361/1‑90 (MQ=255)
gCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGt < 2:415314/90‑1 (MQ=255)
ggggAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTAc < 2:432601/90‑1 (MQ=255)
agGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGaa > 1:644035/1‑90 (MQ=255)
gCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATGACg < 2:587136/90‑1 (MQ=255)
gCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACg > 2:327139/1‑90 (MQ=255)
cACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAgg < 2:146271/90‑1 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCGGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa < 1:670341/90‑1 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa < 2:107119/90‑1 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa < 2:530351/90‑1 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa > 1:653308/1‑90 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa < 1:327139/90‑1 (MQ=255)
cTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCa < 2:375348/90‑1 (MQ=255)
tCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCag > 2:640956/1‑90 (MQ=255)
tCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCag > 1:183237/1‑90 (MQ=255)
gCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGaa < 2:365424/90‑1 (MQ=255)
cGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATAccc > 2:169225/1‑90 (MQ=255)
aCCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGTATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAgcgc > 2:768291/1‑90 (MQ=255)
ctcGGGTCGCCAGTCAGGTCACGGTGCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 2:380310/88‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 2:317043/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTTGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 2:729757/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGTATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 1:768291/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 2:224630/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 2:433471/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 1:677637/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 1:668503/90‑1 (MQ=255)
cACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATc < 1:154217/90‑1 (MQ=255)
cGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTg > 2:735210/1‑90 (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 < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TGCGGCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCATCAGCAT > NZ_CP009273/444428‑444618
|
TGCGGCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGT > SRR3722079.838502/1‑100 (MQ=60)
GCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCG > SRR3722079.436347/1‑100 (MQ=60)
GTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAA > SRR3722079.226543/1‑100 (MQ=60)
GTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAA > SRR3722079.418881/1‑100 (MQ=60)
GTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAA > SRR3722079.136504/1‑100 (MQ=60)
GGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAA > SRR3722079.650689/1‑100 (MQ=60)
AGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCA > SRR3722079.660072/1‑100 (MQ=60)
GGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAG > SRR3722079.184837/1‑100 (MQ=60)
CTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCGGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCC < SRR3722079.677348/100‑1 (MQ=60)
CTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCC < SRR3722079.329759/100‑1 (MQ=60)
CACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGTATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCAC < SRR3722079.776515/100‑1 (MQ=60)
CACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCAC < SRR3722079.155556/100‑1 (MQ=60)
CACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCAC < SRR3722079.675483/100‑1 (MQ=60)
CACGGGTCGCCAGTCAGGTCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCAC < SRR3722079.684749/100‑1 (MQ=60)
TCACAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCtgtc > SRR3722079.129688/1‑96 (MQ=60)
CAGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCATCAGCA > SRR3722079.487447/1‑100 (MQ=60)
AGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCATCAGCAT < SRR3722079.228901/100‑1 (MQ=60)
|
TGCGGCACTACGGCAAAGTTATAGAACGGAGGCGGGGAAGAGGTTGCCCACTCCAGCGTACGGCCACCCCACGGGTCGCCAGTCAGGTCACGGTTCTGGTCGCGGTCGCGAATAGAAACGTACATCTGAATAACGAGGCAGAGAATACCCAGCGCAATCAGTACTGCACCGCTGGCTGCAATCATCAGCAT > NZ_CP009273/444428‑444618
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
