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 |
1,980,420 |
A→G |
G5G (GGA→GGG) |
ftnB → |
non‑heme ferritin‑like protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,980,420 | 0 | A | G | 100.0%
| 56.2
/ NA
| 18 | G5G (GGA→GGG) | ftnB | non‑heme ferritin‑like protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (11/7); total (11/7) |
TTCTGCAAACAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGAATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTGAAC > NZ_CP009273/1980334‑1980505
|
ttCTGCAAACAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATg > 2:435569/1‑90 (MQ=255)
aTGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAaactcaactc < 2:297264/90‑1 (MQ=255)
ggTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACtctc > 1:524380/1‑90 (MQ=255)
ttGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGa > 1:162499/1‑90 (MQ=255)
tCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAAtct > 2:432874/1‑90 (MQ=255)
cTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAAtctc < 2:524380/90‑1 (MQ=255)
ggATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTa > 1:487383/1‑90 (MQ=255)
atatAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTAcc < 2:431352/90‑1 (MQ=255)
tataAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCt < 2:583825/90‑1 (MQ=255)
taAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTc > 1:248871/1‑90 (MQ=255)
taAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTc > 1:291926/1‑90 (MQ=255)
taAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTc > 2:554689/1‑90 (MQ=255)
tatTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCaa < 2:371750/73‑1 (MQ=255)
tatTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCaa > 1:371750/1‑73 (MQ=255)
atTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAg > 2:87503/1‑90 (MQ=255)
tATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTg > 2:187617/1‑90 (MQ=255)
aaCCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTc < 1:432874/90‑1 (MQ=255)
cTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTGAAc < 2:514252/90‑1 (MQ=255)
|
TTCTGCAAACAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGAATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTGAAC > NZ_CP009273/1980334‑1980505
|
| 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
CAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGAATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTGAACAGAGT > NZ_CP009273/1980343‑1980510
|
CAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTC > SRR3722109.532373/1‑100 (MQ=60)
TTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGA > SRR3722109.164513/1‑100 (MQ=60)
tacacattgacattcgtcggcagcgtcagatgtgtataagagacaGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAAC < SRR3722109.10294/55‑1 (MQ=60)
CTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTA > SRR3722109.494731/1‑100 (MQ=60)
CTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTC > SRR3722109.251793/1‑100 (MQ=60)
CTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTC > SRR3722109.295669/1‑100 (MQ=60)
GATATAAGGATATTAGGTATGGCAACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCtgtctc > SRR3722109.376990/1‑94 (MQ=60)
AACCGCTGGGATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTGAACAGAGT < SRR3722109.439262/100‑1 (MQ=60)
|
CAGTAATTATGGTGTTTTGATTTATCTTGCACCTCTCCACTTCTGGATATAAGGATATTAGGTATGGCAACCGCTGGAATGCTTCTCAAACTCAACTCTCAAATGAACCGCGAGTTTTACGCATCCAATCTCTACCTTCACCTGAGTAACTGGTGTTCTGAACAGAGT > NZ_CP009273/1980343‑1980510
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
