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 |
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 | 96.3%
| 96.2
/ ‑3.2
| 27 | intergenic (‑38/‑121) | mgrB/yobH | PhoP/PhoQ regulator MgrB/YobH family protein |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base T (10/16); total (10/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01 |
AGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTA > NZ_CP009273/1902975‑1903147
|
agcaagcCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCa < 2:408530/90‑1 (MQ=255)
agcCAACACCACGGCAACCAGAACGACCCATCGAAACTTTTTCAATCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCg < 1:16821/90‑1 (MQ=255)
acGACAACCAGAACGACCCATCGAAACTTTTTCCCTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc < 2:522805/90‑1 (MQ=255)
acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc < 1:486254/90‑1 (MQ=255)
gACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAg < 1:501146/90‑1 (MQ=255)
aaCCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAgcgc < 2:300993/90‑1 (MQ=255)
aaCCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAgcgc < 1:8139/90‑1 (MQ=255)
aCCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGcc > 2:225154/1‑90 (MQ=255)
aCCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGcc > 2:177642/1‑90 (MQ=255)
ccAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCt < 1:177642/90‑1 (MQ=255)
cAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTa < 1:47808/90‑1 (MQ=255)
aCGCCCCCTCGAAACTTTTTCACTCCAATCCCCGTTTCACCTACCTTCTGTCATTAAACTTGCATGCGTTAGTCAAACAGCGCCTAACTa < 1:533781/90‑1 (MQ=255)
aCGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTa < 2:154177/90‑1 (MQ=255)
aCCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGt > 1:290798/1‑90 (MQ=255)
aaCTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCg > 1:169738/1‑90 (MQ=255)
tttCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCtt < 2:405335/90‑1 (MQ=255)
cACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCttttt < 2:529263/90‑1 (MQ=255)
cAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGaa < 2:451185/90‑1 (MQ=255)
ccGTTTCACCTACCTTATGTCATTAAACTTGCATGCg < 1:166798/37‑1 (MQ=38)
ccGTTTCACCTACCTTATGTCATTAAACTTGCATGCg > 2:166798/1‑37 (MQ=38)
acctTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAg < 1:504538/90‑1 (MQ=255)
tATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTTGCTTGCTTCAGCGCa > 2:8362/1‑90 (MQ=255)
aTGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCat > 2:452806/1‑90 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc > 2:401093/1‑90 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc > 1:284307/1‑90 (MQ=255)
ttAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGcc > 2:389354/1‑90 (MQ=255)
aCTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTa < 1:90879/90‑1 (MQ=255)
|
AGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTA > NZ_CP009273/1902975‑1903147
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 31 ≤ 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
AGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAGCG > NZ_CP009273/1902979‑1903157
|
acattgacattcgtcggcagcgtcagatgtgtataagagacagACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAC < SRR3722111.168892/57‑1 (MQ=60)
AGCCAACACCACGGCAACCAGAACGACCCATCGAAACTTTTTCAATCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAC < SRR3722111.17032/100‑1 (MQ=60)
ACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAAC < SRR3722111.493723/100‑1 (MQ=60)
GACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTA < SRR3722111.508876/100‑1 (MQ=60)
AACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGT > SRR3722111.294510/1‑100 (MQ=60)
AACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGT < SRR3722111.8243/100‑1 (MQ=60)
CCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCC < SRR3722111.179871/100‑1 (MQ=60)
CAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGA < SRR3722111.48389/100‑1 (MQ=60)
ACGCCCCCTCGAAACTTTTTCACTCCAATCCCCGTTTCACCTACCTTCTGTCATTAAACTTGCATGCGTTAGTCAAACAGCGCCTAACTATGTCGATATC < SRR3722111.542152/100‑1 (MQ=60)
GACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCG > SRR3722111.171866/1‑100 (MQ=60)
ACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGC > SRR3722111.287901/1‑100 (MQ=60)
ACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGC < SRR3722111.512327/100‑1 (MQ=60)
ACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAGCG < SRR3722111.92005/100‑1 (MQ=60)
|
AGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAGCG > NZ_CP009273/1902979‑1903157
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
