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 I197 R1
|
189 |
12.7 |
697584 |
97.1% |
677354 |
86.2 |
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%
| 21.0
/ NA
| 8 | K405E (AAA→GAA) | preA | NAD‑dependent dihydropyrimidine dehydrogenase subunit PreA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (3/5); total (3/5) |
GAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATG > NZ_CP009273/2229869‑2230020
|
gagaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGTCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaa > 1:343163/1‑90 (MQ=255)
gagaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaa > 2:339063/1‑90 (MQ=255)
gagaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaa > 2:86350/1‑90 (MQ=255)
gagaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCAGGGAAGTGAAGTTTAAGAAAGGCGaggaa > 1:347079/1‑90 (MQ=255)
tgtgtgGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAacac < 1:88996/90‑1 (MQ=255)
ttGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAAc < 1:271290/90‑1 (MQ=255)
tttGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTaaa < 1:33136/90‑1 (MQ=255)
gAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTc > 2:117147/1‑90 (MQ=255)
gCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGc > 2:208496/1‑90 (MQ=255)
cGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCgg > 1:50821/1‑90 (MQ=255)
ggAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATg < 1:310800/90‑1 (MQ=255)
ggAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATg < 2:347079/90‑1 (MQ=255)
|
GAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATG > NZ_CP009273/2229869‑2230020
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
TTGTAATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAA > NZ_CP009273/2229859‑2230049
|
TTGTAATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGTCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAA > SRR3722076.348388/1‑100 (MQ=60)
TTGTAATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCAGGGAAGTGAAGTTTAAGAAAGGCGAGGAA > SRR3722076.352367/1‑100 (MQ=60)
TGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGT < SRR3722076.90093/100‑1 (MQ=60)
TTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAAC < SRR3722076.275271/100‑1 (MQ=60)
TTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACG < SRR3722076.33528/100‑1 (MQ=60)
GTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGG > SRR3722076.51449/1‑100 (MQ=60)
GGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAAC < SRR3722076.315506/100‑1 (MQ=60)
GGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAA > SRR3722076.242390/1‑100 (MQ=60)
|
TTGTAATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAA > NZ_CP009273/2229859‑2230049
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
