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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,439,101 |
T→C |
K255E (AAG→GAG) |
mepA ← |
penicillin‑insensitive murein endopeptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,439,101 | 0 | T | C | 100.0%
| 35.3
/ NA
| 11 | K255E (AAG→GAG) | mepA | penicillin‑insensitive murein endopeptidase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (6/5); total (6/5) |
TAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTTCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTAAAGGT > NZ_CP009273/2439015‑2439186
|
tAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTctcctc < 1:6691/90‑1 (MQ=255)
aaaCAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCa < 1:102210/90‑1 (MQ=255)
ggCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCtt > 1:37415/1‑90 (MQ=255)
ggCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCtt > 2:39825/1‑90 (MQ=255)
tCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGtt > 1:162456/1‑90 (MQ=255)
cGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCaa > 1:302253/1‑90 (MQ=255)
aGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGc < 2:274162/90‑1 (MQ=255)
gcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCt < 1:194550/90‑1 (MQ=255)
gcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCt < 1:194551/90‑1 (MQ=255)
gcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCt > 2:37675/1‑90 (MQ=255)
gAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATg < 2:162456/90‑1 (MQ=255)
ggTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCggg > 2:180098/1‑89 (MQ=255)
ttctcctCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTAAAGGt < 1:4181/90‑1 (MQ=255)
|
TAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTTCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTAAAGGT > NZ_CP009273/2439015‑2439186
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ 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
ACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTTCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTAAAGGTTGATCTTCAC > NZ_CP009273/2439011‑2439196
|
ACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTT > SRR3722090.37800/1‑100 (MQ=60)
TAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTT < SRR3722090.6763/100‑1 (MQ=60)
AAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTG < SRR3722090.103307/100‑1 (MQ=60)
ATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTT > SRR3722090.164095/1‑100 (MQ=60)
CATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAA > SRR3722090.306103/1‑100 (MQ=60)
GCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCATC < SRR3722090.196679/100‑1 (MQ=60)
GCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAAC < SRR3722090.196678/100‑1 (MQ=60)
TTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTAAAGGTTGATCTTCAC < SRR3722090.4225/100‑1 (MQ=60)
|
ACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTTCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTAAAGGTTGATCTTCAC > NZ_CP009273/2439011‑2439196
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
