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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
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 | 95.8%
| 88.2
/ ‑3.2
| 24 | 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 (18/5); total (18/6) |
| Fisher's exact test for biased strand distribution p-value = 2.50e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTA > NZ_CP009273/1902981‑1903147
|
ccAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCgtt < 2:501857/90‑1 (MQ=255)
acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc > 2:504865/1‑90 (MQ=255)
acGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAAc < 2:399935/90‑1 (MQ=255)
gACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAg < 2:179163/90‑1 (MQ=255)
aaCCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAgcgc < 1:59875/90‑1 (MQ=255)
aCCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGcc > 1:203391/1‑90 (MQ=255)
cAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTa > 2:149122/1‑90 (MQ=255)
aaCGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACt > 1:417791/1‑90 (MQ=255)
tCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGata > 2:338644/1‑90 (MQ=255)
ttttCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCt > 1:236453/1‑90 (MQ=255)
tttCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCtt > 2:115977/1‑90 (MQ=255)
ccGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGTTATTCGTGCTTTTTCGGAATGAGTc > 2:191970/1‑90 (MQ=255)
cGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCg > 1:33018/1‑90 (MQ=255)
tttCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCgct > 2:81178/1‑90 (MQ=255)
tacctTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCa > 1:400169/1‑90 (MQ=255)
aTGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCat > 1:243406/1‑90 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTc > 1:550394/1‑78 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTc < 2:550394/78‑1 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc > 1:172436/1‑90 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc > 2:130252/1‑90 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc > 2:139576/1‑90 (MQ=255)
aTTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGc > 1:266569/1‑90 (MQ=255)
ttAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGcc > 2:102707/1‑90 (MQ=255)
aCTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTa < 1:336987/90‑1 (MQ=255)
|
CCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTA > NZ_CP009273/1902981‑1903147
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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
CACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAGCG > NZ_CP009273/1902985‑1903157
|
CACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCC > SRR3722109.205862/1‑100 (MQ=60)
CGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACT > SRR3722109.423907/1‑100 (MQ=60)
AACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGT < SRR3722109.60593/100‑1 (MQ=60)
CATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCT > SRR3722109.239248/1‑100 (MQ=60)
CTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCG > SRR3722109.33408/1‑100 (MQ=60)
CCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCA > SRR3722109.405951/1‑100 (MQ=60)
CACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCAT > SRR3722109.246270/1‑100 (MQ=60)
ACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTct > SRR3722109.558758/1‑98 (MQ=60)
ACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGC > SRR3722109.174566/1‑100 (MQ=60)
ACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGC > SRR3722109.269864/1‑100 (MQ=60)
TCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGA > SRR3722109.11466/1‑100 (MQ=60)
ACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAGCG < SRR3722109.341451/100‑1 (MQ=60)
|
CACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAGCG > NZ_CP009273/1902985‑1903157
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
