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 |
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 | 92.0%
| 61.6
/ ‑0.2
| 25 | K255E (AAG→GAG) | mepA | penicillin‑insensitive murein endopeptidase |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (16/7); total (17/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.05e-01 |
AAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTTCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTAAAGG > NZ_CP009273/2439016‑2439185
|
aaaCAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCa < 2:124370/90‑1 (MQ=255)
ggCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCa > 2:577174/1‑85 (MQ=255)
ggCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCa < 1:577174/85‑1 (MQ=255)
ggCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCGGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCtt > 1:343845/1‑90 (MQ=255)
ggCTATTAAACCTTTCCATTCGACCACGAGCTCATGCAGGGGGGCCTGACAGGAAGGCGGCAACGGAGGAGGATGCTTCTCCTCAGGCtt > 1:191263/1‑90 (MQ=255)
gCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGCGTCTTCTCCTCAGGCttt > 1:568433/1‑90 (MQ=255)
aTTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTttgtt > 2:452897/1‑90 (MQ=255)
cGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTccc < 1:202061/90‑1 (MQ=255)
cGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTccc > 2:303580/1‑90 (MQ=255)
cGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTccc > 2:242258/1‑90 (MQ=255)
tttCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCgg > 2:448154/1‑90 (MQ=255)
tCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGtt > 2:152313/1‑90 (MQ=255)
tCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGtt > 2:504636/1‑90 (MQ=255)
tGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAAc > 2:410647/1‑90 (MQ=255)
gCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAAcc < 1:393861/90‑1 (MQ=255)
cATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGc < 1:287158/90‑1 (MQ=255)
cATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGc < 2:364541/90‑1 (MQ=255)
tCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCtt > 1:20485/1‑90 (MQ=255)
gcgcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGtt > 1:214341/1‑90 (MQ=255)
cgcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTc > 2:60902/1‑90 (MQ=255)
gcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTTCTCa < 2:38010/42‑1 (MQ=255)
gcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTTCTCa > 1:38010/1‑42 (MQ=255)
gcCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCt > 2:582106/1‑90 (MQ=255)
cggcAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCGCCGCAACCATc > 1:69253/1‑90 (MQ=255)
gtgtCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTa < 2:488320/90‑1 (MQ=255)
cttctcctCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTAAAgg > 2:177603/1‑90 (MQ=255)
|
AAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTTCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTAAAGG > NZ_CP009273/2439016‑2439185
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ 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
GCGGGGAAACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTTCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTAAAGGTTGATCTTCACACT > NZ_CP009273/2439003‑2439199
|
GCGGGGAAACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGGGTCTTCTCC > SRR3722111.55497/1‑100 (MQ=60)
ACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCGGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTT > SRR3722111.348449/1‑100 (MQ=60)
ACCATAAACAGGCTATTAAACCTTTCCATTCGACCACGAGCTCATGCAGGGGGGCCTGACAGGAAGGCGGCAACGGAGGAGGATGCTTCTCCTCAGGCTT > SRR3722111.193653/1‑100 (MQ=22)
CCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGCGTCTTCTCCTCAGGCTTT > SRR3722111.577373/1‑100 (MQ=60)
AAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTG < SRR3722111.586232/100‑1 (MQ=60)
CGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAG < SRR3722111.204568/100‑1 (MQ=60)
CACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTT > SRR3722111.20741/1‑100 (MQ=60)
GCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAG < SRR3722111.399570/100‑1 (MQ=60)
GCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTT > SRR3722111.216952/1‑100 (MQ=60)
CATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTC < SRR3722111.290809/100‑1 (MQ=60)
ATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTTCTCAGGCTTTGTTGctgtctcttatacacatctgacgctgccgacgaatgtc > SRR3722111.38457/1‑62 (MQ=60)
GGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCGCCGCAACCATC > SRR3722111.70069/1‑100 (MQ=60)
TCCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCctgtctcttatacacatctgacgctgccg > SRR3722111.31223/1‑71 (MQ=60)
|
GCGGGGAAACCATAAACAGGCTATTAAACGTTTCCATTAGATCACGTGCTCATCCAGTAGCGCCTGGCAGGAAGGCGGCAACGGAGGCGGTGTCTTCTTCTCAGGCTTTGTTGTTCCCGGTTTTGGAGGTTCAAACCAGCTTTGCAGTTCTGCCCCGCAACCATCGCCTGATGGCGGTAAAGGTTGATCTTCACACT > NZ_CP009273/2439003‑2439199
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
