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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
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%
| 35.3
/ NA
| 12 | K405E (AAA→GAA) | preA | NAD‑dependent dihydropyrimidine dehydrogenase subunit PreA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (6/6); total (6/6) |
GAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGG > NZ_CP009273/2229869‑2230041
|
gagaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaa > 2:144298/1‑90 (MQ=255)
tgtgtgGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAacac < 1:370147/90‑1 (MQ=255)
ggTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTa < 2:356548/90‑1 (MQ=255)
gTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGt > 1:98599/1‑90 (MQ=255)
ttGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGCAACGTTGTa > 1:305458/1‑87 (MQ=255)
ttGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGCAACGTTGTa < 2:305458/87‑1 (MQ=255)
gTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGc > 2:123487/1‑90 (MQ=255)
gCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGc > 1:17470/1‑90 (MQ=255)
gCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGc > 1:242235/1‑90 (MQ=255)
tAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGc < 2:98599/90‑1 (MQ=255)
ggCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATcc > 2:33718/1‑90 (MQ=255)
cGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCgg < 1:123487/90‑1 (MQ=255)
cGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCgg < 2:254209/90‑1 (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
TGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAAAC > NZ_CP009273/2229875‑2230051
|
TGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGT > SRR3722091.100119/1‑100 (MQ=60)
TGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGT < SRR3722091.376682/100‑1 (MQ=60)
GTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGCAACGTTGTAAAA > SRR3722091.310653/1‑100 (MQ=60)
GTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGC > SRR3722091.17722/1‑100 (MQ=60)
GTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGC > SRR3722091.245985/1‑100 (MQ=60)
CGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAAAC < SRR3722091.125351/100‑1 (MQ=60)
|
TGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAAAC > NZ_CP009273/2229875‑2230051
|
| 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: ‑ |
