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 I177 R1
|
141 |
27.5 |
996908 |
97.7% |
973979 |
124.3 |
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%
| 79.7
/ 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 . (11/8); total (11/8) |
TCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGGCGGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTCAGTTGGGCAAAAGCA > NZ_CP009273/467297‑467539
|
tcgtcCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAgg > 2:332494/1‑139 (MQ=255)
gtcCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGgc < 1:332494/138‑1 (MQ=255)
aGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCg > 1:461965/1‑137 (MQ=255)
gcgcTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCt < 1:410700/139‑1 (MQ=255)
cTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGgc > 1:444764/1‑139 (MQ=255)
ggCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAAAGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGGAACCGTGCAACTGGCGGAGCTGGCGCGTAGCAt > 2:447024/1‑139 (MQ=255)
gTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAg < 2:4084/139‑1 (MQ=255)
tGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGc > 1:178206/1‑139 (MQ=255)
tGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGc > 2:45040/1‑139 (MQ=255)
gCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGa < 2:158156/139‑1 (MQ=255)
gTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAAcgcg > 2:290777/1‑78 (MQ=255)
gTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAAcgcg < 1:290777/78‑1 (MQ=255)
cagcaAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGAc > 1:39395/1‑131 (MQ=255)
cagcaAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGAc < 2:39395/131‑1 (MQ=255)
aTCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACAcgccg > 1:80501/1‑139 (MQ=255)
gCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAg > 1:175232/1‑138 (MQ=255)
cTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAg > 1:217102/1‑137 (MQ=255)
cGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAgggg < 1:45040/139‑1 (MQ=255)
aTACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGaat < 2:247505/139‑1 (MQ=255)
ctggggggGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTCAGTTGGGCAAAAGCa < 2:217102/137‑1 (MQ=255)
|
TCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGGCGGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTCAGTTGGGCAAAAGCA > NZ_CP009273/467297‑467539
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
GCCTTGATGGTCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGGCGGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTC > NZ_CP009273/467287‑467524
|
atacgagatctagtacagtctcgtgggctcggagatgtgtataagagacaGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCG < SRR3722131.294121/101‑1 (MQ=60)
CGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCG < SRR3722131.336223/150‑1 (MQ=60)
CGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGG > SRR3722131.466920/1‑149 (MQ=60)
GTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCG > SRR3722131.449530/1‑151 (MQ=60)
CGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCA < SRR3722131.415151/151‑1 (MQ=60)
GCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCG > SRR3722131.180246/1‑151 (MQ=60)
TGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTAC > SRR3722131.39799/1‑151 (MQ=60)
GGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGC > SRR3722131.81387/1‑151 (MQ=60)
GATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGC > SRR3722131.177237/1‑150 (MQ=60)
ATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGC > SRR3722131.219684/1‑149 (MQ=60)
GCGGATACCTTCCTCGCCAACGTGACGCTGGGG‑GGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTC < SRR3722131.45506/151‑1 (MQ=60)
|
GCCTTGATGGTCGTCCATTAAGTTCGCTAAGTCACAGCGCGCTGCGCCAGGGCGTGGCAATGGTGCAGCAAGATCCGGTGGTGCTGGCGGATACCTTCCTCGCCAACGTGACGCTGGGGCGGGATATCTCCGAAGAACGCGTCTGGCAGGCGCTGGAAACCGTGCAACTGGCGGAGCTGGCGCGTAGCATGAGCGACGGTATTTACACGCCGCTGGGCGAGCAGGGGAATAATCTCTC > NZ_CP009273/467287‑467524
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
