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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,840,691 |
T→G |
N432H (AAC→CAC) |
uhpC ← |
MFS transporter family glucose‑6‑phosphate receptor UhpC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,840,691 | 0 | T | G | 100.0%
| 31.4
/ NA
| 11 | N432H (AAC→CAC) | uhpC | MFS transporter family glucose‑6‑phosphate receptor UhpC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (3/8); total (3/8) |
CCAGGCAAAACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTTCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAG > NZ_CP009273/3840604‑3840767
|
ccAGGCAAAACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAGGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCa > 1:57804/1‑90 (MQ=255)
gCAAAACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCaaaaa < 1:428730/90‑1 (MQ=255)
aCCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCa < 1:338601/90‑1 (MQ=255)
gAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAAc < 1:32629/90‑1 (MQ=255)
tatGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCggcggc < 2:289979/90‑1 (MQ=255)
gAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAgaga > 1:418718/1‑90 (MQ=255)
aTGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACaaaa < 2:277939/90‑1 (MQ=255)
cTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTcc < 1:109943/90‑1 (MQ=255)
cTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTcc < 2:418718/90‑1 (MQ=255)
tCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAg < 1:154826/90‑1 (MQ=255)
ggTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCCCAAAAAATCCGCTCCAGTGCCAg > 2:275733/1‑90 (MQ=255)
|
CCAGGCAAAACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTTCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAG > NZ_CP009273/3840604‑3840767
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ 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
GAGATAGCGTCCAGGCAAAACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTTCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGGTATCGAGTAC > NZ_CP009273/3840594‑3840778
|
GAGATAGCGTCCAGGCAAAACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAGGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCA > SRR3722087.58297/1‑100 (MQ=60)
GCAAAACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAAC < SRR3722087.433735/100‑1 (MQ=60)
ACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAG < SRR3722087.342366/100‑1 (MQ=60)
GAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGG < SRR3722087.32892/100‑1 (MQ=60)
GATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGA > SRR3722087.423594/1‑100 (MQ=60)
agatgtgtataagagacaGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCA < SRR3722087.293914/82‑1 (MQ=60)
CTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGGT < SRR3722087.111006/100‑1 (MQ=60)
TCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGGTAT < SRR3722087.156246/100‑1 (MQ=60)
GTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGGTctgtctctt > SRR3722087.36461/1‑91 (MQ=60)
|
GAGATAGCGTCCAGGCAAAACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTTCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGGTATCGAGTAC > NZ_CP009273/3840594‑3840778
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
