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 |
1,682,423 |
G→C |
A71G (GCC→GGC) |
fumB ← |
class I fumarate hydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,682,423 | 0 | G | C | 100.0%
| 33.1
/ NA
| 12 | A71G (GCC→GGC) | fumB | class I fumarate hydratase |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (7/5); total (7/5) |
TTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGC > NZ_CP009273/1682338‑1682499
|
tttCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCAc > 2:482071/1‑90 (MQ=255)
aTGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTgg < 1:589659/90‑1 (MQ=255)
aTGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTgg < 1:81227/90‑1 (MQ=255)
ggAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTgcgc < 2:141078/90‑1 (MQ=255)
tACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGAc > 2:249662/1‑90 (MQ=255)
aCGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACg < 1:482071/90‑1 (MQ=255)
tATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACg > 1:456444/1‑90 (MQ=255)
ttttCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTgg > 1:571152/1‑90 (MQ=255)
ttttCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTgg > 2:350874/1‑90 (MQ=255)
tCACGCAGAATGTCGCCTACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAAc < 1:43813/90‑1 (MQ=255)
tCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACCCATCATGAAACGCCTGGCGCGCCAACAGAGTTAAc > 2:328183/1‑90 (MQ=255)
aCGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGc > 2:536985/1‑90 (MQ=255)
|
TTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGC > NZ_CP009273/1682338‑1682499
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 30 ≤ 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
TGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTG > NZ_CP009273/1682326‑1682507
|
TGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCC < SRR3722109.483477/100‑1 (MQ=60)
ATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGAC < SRR3722109.598585/100‑1 (MQ=60)
ATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGAC < SRR3722109.82226/100‑1 (MQ=60)
ACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAAC < SRR3722109.489325/100‑1 (MQ=60)
GCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACG > SRR3722109.463287/1‑100 (MQ=60)
ATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGG > SRR3722109.579811/1‑100 (MQ=60)
cagatgtgtataagagacagGAATGTCGCCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTT < SRR3722109.146393/80‑1 (MQ=60)
TCACGCAGAATGTCGCCTACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTG < SRR3722109.44334/100‑1 (MQ=60)
|
TGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCATTTTCGCTGGCCTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTG > NZ_CP009273/1682326‑1682507
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
