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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
965,365 |
T→C |
M174T (ATG→ACG) |
ycaQ → |
winged helix DNA‑binding protein YcaQ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 965,365 | 0 | T | C | 100.0%
| 62.9
/ NA
| 18 | M174T (ATG→ACG) | ycaQ | winged helix DNA‑binding protein YcaQ |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/13); total (5/13) |
GGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTC > NZ_CP009273/965292‑965452
|
ggTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCa < 2:571605/91‑1 (MQ=255)
gTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCaa > 1:699956/1‑91 (MQ=255)
tGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAAc > 1:510350/1‑91 (MQ=255)
gCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACt > 2:631226/1‑91 (MQ=255)
cAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACtt > 2:153662/1‑91 (MQ=255)
gggAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTa < 1:304797/91‑1 (MQ=255)
ggAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTAt < 2:218065/91‑1 (MQ=255)
ggAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTAt < 2:427338/91‑1 (MQ=255)
ggAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTAt < 1:277877/91‑1 (MQ=255)
cATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAcc < 1:751076/91‑1 (MQ=255)
cATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAcc < 1:631226/91‑1 (MQ=255)
cATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAcc < 2:439955/91‑1 (MQ=255)
aCGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTc < 1:447232/91‑1 (MQ=255)
aTCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGcc < 2:213677/91‑1 (MQ=255)
tGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGa > 2:887578/1‑91 (MQ=255)
ggAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGAc < 2:699956/91‑1 (MQ=255)
ggAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGAc < 2:715146/91‑1 (MQ=255)
ggAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGAc < 2:899233/91‑1 (MQ=255)
tgacggtgatTGAACGGCGCAACTTCCAGCGCGTTTATGATTTACCCCACCGTGTCATGCCTGAc < 2:508573/65‑1 (MQ=255)
tgacggtgatTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTc > 1:319126/1‑91 (MQ=255)
|
GGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTC > NZ_CP009273/965292‑965452
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
CGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAG > NZ_CP009273/965270‑965460
|
CGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGA < SRR3722125.155819/101‑1 (MQ=60)
TGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAAC < SRR3722125.412275/101‑1 (MQ=60)
CCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAA > SRR3722125.715038/1‑101 (MQ=60)
CTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAAC > SRR3722125.521177/1‑101 (MQ=60)
GGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACC < SRR3722125.311041/101‑1 (MQ=60)
GGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCC < SRR3722125.283497/101‑1 (MQ=60)
CATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCC < SRR3722125.644816/101‑1 (MQ=60)
CATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCC < SRR3722125.767297/101‑1 (MQ=60)
ACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACT < SRR3722125.456676/101‑1 (MQ=60)
GCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGctgtctcttatacaca > SRR3722125.519361/1‑85 (MQ=60)
GCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTC > SRR3722125.325683/1‑101 (MQ=60)
GGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAG > SRR3722125.248285/1‑101 (MQ=60)
|
CGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAG > NZ_CP009273/965270‑965460
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
