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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,903,061 |
A→T |
intergenic (‑38/‑121) |
mgrB ← / → yobH |
PhoP/PhoQ regulator MgrB/YobH family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,903,061 | 0 | A | T | 100.0%
| 171.3
/ NA
| 43 | intergenic (‑38/‑121) | mgrB/yobH | PhoP/PhoQ regulator MgrB/YobH family protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (26/17); total (26/17) |
AGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCC > NZ_CP009273/1902979‑1903143
|
agcCAACACCACGACAACCAGACCGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCg < 1:792896/90‑1 (MQ=255)
acacCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCgttagt > 2:118354/1‑90 (MQ=255)
caccacGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCgttagtt > 1:408997/1‑90 (MQ=255)
accacGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCgttagtta > 2:599105/1‑90 (MQ=255)
ccacGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTaa > 2:718847/1‑90 (MQ=255)
ccacGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTaa < 1:579804/90‑1 (MQ=255)
acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc > 2:809213/1‑90 (MQ=255)
acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc < 2:734916/90‑1 (MQ=255)
acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc > 1:231276/1‑90 (MQ=255)
acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc > 2:869473/1‑90 (MQ=255)
acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc < 2:231276/90‑1 (MQ=255)
acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc < 1:1090111/90‑1 (MQ=255)
acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc > 1:1033461/1‑90 (MQ=255)
aCAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCg > 2:778371/1‑77 (MQ=255)
aCAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCg < 1:778371/77‑1 (MQ=255)
aaCCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAgcgc < 1:537774/90‑1 (MQ=255)
aaCCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAgcgc > 1:621177/1‑90 (MQ=255)
cAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCgttagt > 2:1005362/1‑77 (MQ=255)
cAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCgttagt < 1:1005362/77‑1 (MQ=255)
aaCGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACt > 2:113570/1‑90 (MQ=255)
aCGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTa < 2:58585/90‑1 (MQ=255)
cccATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTc > 1:943651/1‑90 (MQ=255)
aaTCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAAt > 1:1219096/1‑90 (MQ=255)
tcCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGt < 1:447501/90‑1 (MQ=255)
ttCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCgctt < 1:1602/90‑1 (MQ=255)
acctacctTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCgcttgct > 2:254062/1‑90 (MQ=255)
ctacctTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTc < 2:939051/90‑1 (MQ=255)
acctTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAg < 2:370620/90‑1 (MQ=255)
ctTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAgcg > 2:254505/1‑90 (MQ=255)
tATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCa > 2:288911/1‑90 (MQ=255)
aTGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAgcgcgt > 2:63665/1‑88 (MQ=255)
aTGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCat > 1:462069/1‑90 (MQ=255)
aTGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCat > 2:1089047/1‑90 (MQ=255)
aTGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCat < 1:152470/90‑1 (MQ=255)
aTGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCat < 1:113570/90‑1 (MQ=255)
aTGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCat > 2:920034/1‑90 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTc > 2:494463/1‑78 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTc < 1:494463/78‑1 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc > 2:536763/1‑90 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc > 1:307706/1‑90 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc > 1:1120269/1‑90 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc > 2:880760/1‑90 (MQ=255)
ttAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGcc < 1:908731/90‑1 (MQ=255)
|
AGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCC > NZ_CP009273/1902979‑1903143
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAG > NZ_CP009273/1902975‑1903155
|
AGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTT > SRR3722089.413948/1‑100 (MQ=60)
cagCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAC < SRR3722089.788958/97‑1 (MQ=60)
AGCCAACACCACGACAACCAGACCGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAC < SRR3722089.803820/100‑1 (MQ=60)
AGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAC > SRR3722089.1048911/1‑100 (MQ=60)
AGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAC > SRR3722089.234210/1‑100 (MQ=60)
cagCCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGC < SRR3722089.1020330/97‑1 (MQ=60)
ACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGC > SRR3722089.628995/1‑100 (MQ=60)
CCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTA < SRR3722089.586735/100‑1 (MQ=60)
ACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAAC < SRR3722089.1106558/100‑1 (MQ=60)
AACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGT < SRR3722089.544038/100‑1 (MQ=60)
ACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTC > SRR3722089.957481/1‑100 (MQ=60)
TTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAAT > SRR3722089.1237643/1‑100 (MQ=60)
TCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTC < SRR3722089.452867/100‑1 (MQ=60)
TTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGC < SRR3722089.1617/100‑1 (MQ=60)
CACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCAT > SRR3722089.467584/1‑100 (MQ=60)
agACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATT < SRR3722089.500325/98‑1 (MQ=60)
ACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGC > SRR3722089.1137257/1‑100 (MQ=60)
ACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGC > SRR3722089.311609/1‑100 (MQ=60)
ATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTA < SRR3722089.154367/100‑1 (MQ=60)
ATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTA < SRR3722089.114957/100‑1 (MQ=60)
TCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGA > SRR3722089.1189916/1‑100 (MQ=60)
CATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTctgtctcttatacacatctgacgctgc > SRR3722089.1111540/1‑73 (MQ=60)
ATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATT < SRR3722089.758637/100‑1 (MQ=60)
ATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATT > SRR3722089.772868/1‑100 (MQ=60)
TTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTA < SRR3722089.921944/100‑1 (MQ=60)
AAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAG > SRR3722089.1066612/1‑100 (MQ=60)
|
AGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAG > NZ_CP009273/1902975‑1903155
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
