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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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%
| 85.1
/ NA
| 25 | K255E (AAG→GAG) | mepA | penicillin‑insensitive murein endopeptidase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (17/8); total (17/8) |
TAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑TCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCG > NZ_CP009273/2439015‑2439178
|
tAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTct‑‑cctc > 1:363273/1‑90 (MQ=255)
ggCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGc > 1:40113/1‑88 (MQ=255)
ggCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGc < 2:40113/88‑1 (MQ=255)
ggCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCtt > 2:448482/1‑90 (MQ=255)
cGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTccc < 2:537541/90‑1 (MQ=255)
tttCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCgg > 1:222582/1‑90 (MQ=255)
tttCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCgg > 2:560670/1‑90 (MQ=255)
ttCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGGGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGt > 1:577779/1‑90 (MQ=255)
tCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGtt > 2:593850/1‑90 (MQ=255)
tCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGtt > 2:347295/1‑90 (MQ=255)
aCGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCa > 2:421169/1‑90 (MQ=255)
tGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGa > 2:276582/1‑81 (MQ=255)
tGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGa < 1:276582/81‑1 (MQ=255)
tGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAAc > 2:452708/1‑90 (MQ=255)
tGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAAc > 1:270538/1‑90 (MQ=255)
gCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAAcc > 1:165142/1‑90 (MQ=255)
tCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAAcc > 1:79387/1‑90 (MQ=255)
gcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCt > 1:408205/1‑90 (MQ=255)
gcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGGTCAAACCAGCTTTGCAGTTCt > 1:54979/1‑90 (MQ=255)
tGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGcc > 1:591539/1‑90 (MQ=255)
aGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGc < 2:728033/90‑1 (MQ=255)
gAAGGCGGCAACGGAGGCGGTGTCTTCTCCCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGc < 2:79387/90‑1 (MQ=255)
cggcAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATc < 2:165142/90‑1 (MQ=255)
gcAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGc < 2:705968/90‑1 (MQ=255)
gAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATg < 2:408268/90‑1 (MQ=255)
gCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCg > 1:457738/1‑90 (MQ=255)
|
TAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑TCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCG > NZ_CP009273/2439015‑2439178
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ 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
GCGGGGAAACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑TCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCG > NZ_CP009273/2439003‑2439178
|
GCGGGGAAACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CC < SRR3722073.20522/100‑1 (MQ=60)
GGGGAAACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTC > SRR3722073.370983/1‑100 (MQ=60)
ACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTT > SRR3722073.41088/1‑100 (MQ=60)
ACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTT < SRR3722073.544468/100‑1 (MQ=60)
CTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGG > SRR3722073.227197/1‑100 (MQ=60)
TATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGGGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGT > SRR3722073.589849/1‑100 (MQ=60)
TTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAAC > SRR3722073.276262/1‑100 (MQ=60)
TAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACC > SRR3722073.168422/1‑100 (MQ=60)
TAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACC < SRR3722073.282434/100‑1 (MQ=60)
GATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACC > SRR3722073.81198/1‑100 (MQ=60)
ATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCT > SRR3722073.416927/1‑100 (MQ=60)
ATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGGTCAAACCAGCTTTGCAGTTCT > SRR3722073.56274/1‑100 (MQ=60)
CAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCC > SRR3722073.603898/1‑100 (MQ=60)
GGCAACGGAGGCGGTGTCTTCT‑‑CCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCG > SRR3722073.467508/1‑100 (MQ=60)
|
GCGGGGAAACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCT‑‑TCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCG > NZ_CP009273/2439003‑2439178
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
