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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
502,414 |
T→C |
D42G (GAT→GGT) |
ybaK ← |
Cys‑tRNA(Pro)/Cys‑tRNA(Cys) deacylase YbaK |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 502,414 | 0 | T | C | 100.0%
| 34.6
/ NA
| 12 | D42G (GAT→GGT) | ybaK | Cys‑tRNA(Pro)/Cys‑tRNA(Cys) deacylase YbaK |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (7/5); total (7/5) |
CCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTAT > NZ_CP009273/502328‑502486
|
ccAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCg > 2:452144/1‑90 (MQ=255)
atatCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGtt < 2:525295/90‑1 (MQ=255)
atCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTc > 1:417291/1‑90 (MQ=255)
tCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCa > 1:117417/1‑90 (MQ=255)
aCCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGc > 1:359444/1‑90 (MQ=255)
gTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGttt < 1:513878/83‑1 (MQ=255)
gTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGttt > 2:513878/1‑83 (MQ=255)
aCTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCg < 1:484581/90‑1 (MQ=255)
aCTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCg < 1:528512/90‑1 (MQ=255)
cagcGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGt > 2:363777/1‑90 (MQ=255)
cagcGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGt > 2:482229/1‑90 (MQ=255)
gcGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTAt < 2:53093/90‑1 (MQ=255)
|
CCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTAT > NZ_CP009273/502328‑502486
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTTTTTTAAGATCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAAA > NZ_CP009273/502316‑502501
|
CTTTTTTAAGATCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACC < SRR3722111.479822/100‑1 (MQ=60)
TTTTTTAAGATCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCC < SRR3722111.147981/100‑1 (MQ=60)
GGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTC > SRR3722111.423446/1‑100 (MQ=60)
GTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCA > SRR3722111.118894/1‑100 (MQ=60)
GTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGC > SRR3722111.364413/1‑100 (MQ=60)
TATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATC < SRR3722111.521878/100‑1 (MQ=60)
ACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGG < SRR3722111.492014/100‑1 (MQ=60)
ACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGG < SRR3722111.536807/100‑1 (MQ=60)
TTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAAA > SRR3722111.38228/1‑100 (MQ=60)
|
CTTTTTTAAGATCCAGTTGACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACGAAA > NZ_CP009273/502316‑502501
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
