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 I184 R1
|
278 |
29.6 |
1166432 |
97.3% |
1134938 |
124.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
928,200 |
T→C |
R50R (CGT→CGC) |
lrp → |
leucine‑responsive transcriptional regulator Lrp |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 928,200 | 0 | T | C | 100.0%
| 133.8
/ NA
| 39 | R50R (CGT→CGC) | lrp | leucine‑responsive transcriptional regulator Lrp |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (19/20); total (19/20) |
AGAAGCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATAC > NZ_CP009273/928064‑928334
|
agaagCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCg < 2:470217/139‑1 (MQ=255)
gCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACa < 2:222862/139‑1 (MQ=255)
cGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTAtt > 1:184852/1‑139 (MQ=255)
cGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTAtt > 2:249528/1‑139 (MQ=255)
gACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCTTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTAtt < 2:179870/138‑1 (MQ=255)
ccGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAg < 2:372658/139‑1 (MQ=255)
tATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACa < 2:58281/123‑1 (MQ=255)
tATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACa > 1:58281/1‑123 (MQ=255)
tATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGc > 2:569329/1‑139 (MQ=255)
aaCATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGgcgc > 1:438040/1‑139 (MQ=255)
ttAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTaa > 1:363812/1‑139 (MQ=255)
ttGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCAt > 1:22005/1‑138 (MQ=255)
tGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTa > 1:341696/1‑139 (MQ=255)
ggCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCAt > 2:386952/1‑138 (MQ=255)
ggCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCAt < 2:341696/138‑1 (MQ=255)
tATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACtt < 2:488300/139‑1 (MQ=255)
ttCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACa < 2:65328/78‑1 (MQ=255)
ttCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACa > 1:65328/1‑78 (MQ=255)
tCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGt < 1:426465/139‑1 (MQ=255)
cTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTgaga < 2:22005/139‑1 (MQ=255)
cTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTGGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACGTCTGGTATTCGTTgaga < 1:339545/139‑1 (MQ=255)
cTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTAc > 1:403852/1‑139 (MQ=255)
aaCGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTAct < 1:510464/137‑1 (MQ=255)
tgGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGt > 1:107340/1‑57 (MQ=255)
tgGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGt < 2:107340/57‑1 (MQ=255)
tgGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAggg > 2:317726/1‑67 (MQ=255)
tgGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAggg < 1:317726/67‑1 (MQ=255)
tgGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTa < 1:30829/94‑1 (MQ=255)
tgGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTa > 2:30829/1‑94 (MQ=255)
gACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTgg < 2:438040/139‑1 (MQ=255)
ccccAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCAcc > 2:506078/1‑139 (MQ=255)
tGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGgcg < 1:530670/57‑1 (MQ=255)
tGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGgcg > 2:530670/1‑57 (MQ=255)
tGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGttt > 2:508615/1‑138 (MQ=255)
tGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGttt > 1:475261/1‑138 (MQ=255)
ccTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTCCTCTGAATCGTGGCGCACCGGATGTGTTTGaa < 1:508615/139‑1 (MQ=255)
gAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACaa < 1:249528/138‑1 (MQ=255)
tgCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATAc > 2:494534/1‑139 (MQ=255)
tgCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATAc < 2:475261/139‑1 (MQ=255)
|
AGAAGCGCCCTGGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATAC > NZ_CP009273/928064‑928334
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATACCGCTGTAC > NZ_CP009273/928075‑928342
|
GGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTC > SRR3722139.187132/1‑151 (MQ=60)
GATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCctgtct > SRR3722139.58942/1‑145 (MQ=60)
cagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGC < SRR3722139.321651/89‑1 (MQ=60)
GTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCT > SRR3722139.443189/1‑151 (MQ=60)
TCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAAC > SRR3722139.368184/1‑151 (MQ=60)
tttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCC < SRR3722139.536775/79‑1 (MQ=60)
TTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATT > SRR3722139.22242/1‑150 (MQ=60)
TCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTAT > SRR3722139.345851/1‑151 (MQ=60)
ggtctcgtgggctcggagatgtgtataagagacagTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCAT < SRR3722139.31177/116‑1 (MQ=60)
GATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtat > SRR3722139.66114/1‑100 (MQ=60)
CGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACT > SRR3722139.408638/1‑151 (MQ=60)
GTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTC < SRR3722139.431484/151‑1 (MQ=60)
GCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTGGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACGTCTGGTATTCGTTGAGATTACTCTGAAT < SRR3722139.343676/151‑1 (MQ=60)
TTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaa > SRR3722139.108656/1‑79 (MQ=60)
AAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGG < SRR3722139.516342/149‑1 (MQ=60)
CCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTG > SRR3722139.480794/1‑150 (MQ=60)
GCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTCCTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATAC < SRR3722139.514479/151‑1 (MQ=60)
TGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATACCGC < SRR3722139.252688/150‑1 (MQ=60)
CGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATACCGCTGTAC > SRR3722139.204157/1‑151 (MQ=60)
|
GGCAAAGATCTCGACCGTATCGATCGTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAATCGTGGCGCACCGGATGTGTTTGAACAATTCAATACCGCTGTAC > NZ_CP009273/928075‑928342
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
