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 |
|
A2 F5 I178 R1
|
167 |
28.0 |
1137820 |
95.3% |
1084342 |
115.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
467,406 |
Δ1 bp |
coding (1315/1782 nt) |
mdlB → |
SmdB family multidrug efflux ABC transporter permease/ATP‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 467,406 | 0 | C | . | 100.0%
| 81.0
/ NA
| 19 | coding (1315/1782 nt) | mdlB | SmdB family multidrug efflux ABC transporter permease/ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (7/12); total (7/12) |
CTTGATGGTCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGGCGGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTC > NZ_CP009273/467289‑467522
|
cTTGATGGTCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGt < 1:331541/139‑1 (MQ=255)
tGGTCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGc < 1:141928/139‑1 (MQ=255)
gtcgtcCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAg < 2:478568/139‑1 (MQ=255)
cGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTg > 2:292830/1‑139 (MQ=255)
gcTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTgg < 1:550013/139‑1 (MQ=255)
cgcCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGcgcg < 1:145368/139‑1 (MQ=255)
cAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGAc < 2:443080/139‑1 (MQ=255)
caAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTacac < 2:352712/139‑1 (MQ=255)
tgCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAg < 2:322120/139‑1 (MQ=255)
gCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAg < 1:355722/110‑1 (MQ=255)
gCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAg > 2:355722/1‑110 (MQ=255)
gCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACAcgcc > 1:465202/1‑128 (MQ=255)
gCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACAcgcc < 2:465202/128‑1 (MQ=255)
cGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAg > 1:290377/1‑61 (MQ=255)
cGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAg < 2:290377/61‑1 (MQ=255)
aTACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGaat < 1:292830/139‑1 (MQ=255)
tACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGaat > 1:364977/1‑138 (MQ=255)
tCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAAtctc > 2:487688/1‑139 (MQ=255)
tCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAAtctc > 2:110765/1‑139 (MQ=255)
|
CTTGATGGTCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGGCGGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTC > NZ_CP009273/467289‑467522
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCTTGATGGTCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGGCGGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTCAGTTGGGCAAAAGCAACTGCTGGCACTGGCGC > NZ_CP009273/467288‑467556
|
CCTTGATGGTCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGC < SRR3722132.337734/151‑1 (MQ=60)
ATGGTCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAA < SRR3722132.144531/151‑1 (MQ=60)
CGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATG < SRR3722132.559698/151‑1 (MQ=60)
CTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgctt > SRR3722132.365011/1‑86 (MQ=60)
GCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCG < SRR3722132.148051/151‑1 (MQ=60)
agatgtgtataagagacagGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTT < SRR3722132.362291/132‑1 (MQ=60)
GATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCC > SRR3722132.473535/1‑151 (MQ=60)
GGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCtgtctcttatacacatctccgagcccacgagaccgtactagatttcgtatgccgtcttctgcttga > SRR3722132.295893/1‑84 (MQ=60)
GTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATA > SRR3722132.371680/1‑150 (MQ=60)
GATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTCAGT < SRR3722132.298393/151‑1 (MQ=60)
GGGGGGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTCAGTTGGGCAAAAGCAACTGCTGGCACTGG > SRR3722132.396896/1‑151 (MQ=60)
GGGGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTCAGTTGGGCAAAAGCAACTGCTGGCACTGGCG < SRR3722132.436859/151‑1 (MQ=60)
GGGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTCAGTTGGGCAAAAGCAACTGCTGGCACTGGCGC > SRR3722132.528373/1‑151 (MQ=60)
|
CCTTGATGGTCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGGCGGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTCAGTTGGGCAAAAGCAACTGCTGGCACTGGCGC > NZ_CP009273/467288‑467556
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
