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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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%
| 53.0
/ NA
| 17 | 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 (8/9); total (8/9) |
ACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACG > NZ_CP009273/502335‑502498
|
aCCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCaa > 2:116996/1‑90 (MQ=255)
tttCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAAtt < 1:74254/90‑1 (MQ=255)
atatCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGtt < 1:36094/90‑1 (MQ=255)
atatCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGtt < 2:200250/90‑1 (MQ=255)
tCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCa > 1:326103/1‑90 (MQ=255)
tCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCa > 1:50994/1‑90 (MQ=255)
tCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCa > 1:590/1‑90 (MQ=255)
ccGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGcc < 1:453912/90‑1 (MQ=255)
tCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGAt < 2:326103/90‑1 (MQ=255)
cTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCg > 2:390857/1‑89 (MQ=255)
cTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCg < 1:390857/89‑1 (MQ=255)
gCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGc < 1:224601/90‑1 (MQ=255)
gCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGc > 2:251086/1‑90 (MQ=255)
caccaGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTc < 2:590/90‑1 (MQ=255)
accaGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCg > 1:403269/1‑90 (MQ=255)
cagcagCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTa < 1:218025/90‑1 (MQ=255)
ccTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACg > 1:466300/1‑90 (MQ=255)
|
ACCTGCGACCGGCGTAACGGCCACGGCAAGGTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACG > NZ_CP009273/502335‑502498
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACG > NZ_CP009273/502365‑502498
|
GTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCA > SRR3722094.331397/1‑100 (MQ=60)
GTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCA > SRR3722094.51700/1‑100 (MQ=60)
GTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCA > SRR3722094.598/1‑100 (MQ=60)
TTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCC < SRR3722094.75312/100‑1 (MQ=60)
ATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGAT < SRR3722094.36602/100‑1 (MQ=60)
CCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCT < SRR3722094.461900/100‑1 (MQ=60)
GTTCACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCG > SRR3722094.410250/1‑100 (MQ=60)
ACTGCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGG < SRR3722094.397574/100‑1 (MQ=60)
GCCACCAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTAT < SRR3722094.227620/100‑1 (MQ=60)
CAGCAGCGTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATT < SRR3722094.220962/100‑1 (MQ=60)
GTTTTGTAGACCTGACCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACG > SRR3722094.474525/1‑100 (MQ=60)
|
GTGTTTCATATCACCGTTCACTGCCACCAGCAGCGTTTTGTAGACCTGATCCGGATTCAAACCTAATTTTTTGACGACTTCATCGCCAAAATTGGTTTCAGCCGGATCGTGCTCGTAGGTATGGATTTGAAACG > NZ_CP009273/502365‑502498
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
