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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,229,956 |
A→G |
K405E (AAA→GAA) |
preA → |
NAD‑dependent dihydropyrimidine dehydrogenase subunit PreA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,229,956 | 0 | A | G | 100.0%
| 42.0
/ NA
| 14 | K405E (AAA→GAA) | preA | NAD‑dependent dihydropyrimidine dehydrogenase subunit PreA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (8/6); total (8/6) |
GAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGG > NZ_CP009273/2229869‑2230041
|
gagaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaa > 2:64200/1‑90 (MQ=255)
gagaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaa > 1:386477/1‑90 (MQ=255)
gagaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaa > 2:123272/1‑90 (MQ=255)
gtgtgGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACAcc > 2:479650/1‑90 (MQ=255)
gtgtgGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACAcc > 1:20783/1‑90 (MQ=255)
tCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGtt > 2:382661/1‑90 (MQ=255)
gCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTa < 1:64200/90‑1 (MQ=255)
cACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAgaga > 1:8900/1‑90 (MQ=255)
cACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAgaga > 1:95562/1‑90 (MQ=255)
gCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATcc > 2:440700/1‑90 (MQ=255)
tGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGtt < 1:464576/90‑1 (MQ=255)
aTTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCt > 1:402333/1‑90 (MQ=255)
cGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCgg > 1:159567/1‑90 (MQ=255)
gggAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGAt < 1:491791/90‑1 (MQ=255)
gtTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGaa < 2:449716/90‑1 (MQ=255)
ggCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATcc < 1:110167/90‑1 (MQ=255)
cGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCgg < 1:123272/90‑1 (MQ=255)
|
GAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGG > NZ_CP009273/2229869‑2230041
|
| 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
TTGTAATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAAAC > NZ_CP009273/2229859‑2230051
|
TTGTAATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAA > SRR3722114.391154/1‑100 (MQ=60)
AATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAAC < SRR3722114.130864/100‑1 (MQ=60)
ACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACC > SRR3722114.20991/1‑100 (MQ=60)
GCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGA < SRR3722114.64845/100‑1 (MQ=60)
GCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGA > SRR3722114.8987/1‑100 (MQ=60)
GCTTCGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGA > SRR3722114.96571/1‑100 (MQ=60)
GGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCT > SRR3722114.407231/1‑100 (MQ=60)
TGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCG < SRR3722114.470379/100‑1 (MQ=60)
GTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGG > SRR3722114.161162/1‑100 (MQ=60)
GGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAA < SRR3722114.497940/100‑1 (MQ=60)
GGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAA < SRR3722114.111332/100‑1 (MQ=60)
CGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAAAC < SRR3722114.124563/100‑1 (MQ=60)
|
TTGTAATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAAAC > NZ_CP009273/2229859‑2230051
|
| 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: ‑ |
