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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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%
| 78.7
/ NA
| 23 | K405E (AAA→GAA) | preA | NAD‑dependent dihydropyrimidine dehydrogenase subunit PreA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/10); total (13/10) |
GAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGG > NZ_CP009273/2229869‑2230041
|
gagaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaa > 2:229798/1‑90 (MQ=255)
gaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaaga > 2:394713/1‑90 (MQ=255)
gaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaaga > 2:38456/1‑90 (MQ=255)
gaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaaga > 1:471352/1‑90 (MQ=255)
gaAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGaggaaga > 1:531840/1‑90 (MQ=255)
aaTGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAac < 1:276605/90‑1 (MQ=255)
gtgtgGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACAcc > 2:362195/1‑90 (MQ=255)
tGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACg < 2:472593/90‑1 (MQ=255)
cACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAgaga > 1:107233/1‑90 (MQ=255)
cGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACg < 2:519116/90‑1 (MQ=255)
gCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATcc > 2:446283/1‑90 (MQ=255)
gCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATc < 1:588277/89‑1 (MQ=255)
gCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATc > 2:588277/1‑89 (MQ=255)
gTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCAt > 2:186185/1‑90 (MQ=255)
gAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTa < 2:323873/56‑1 (MQ=255)
gAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTa > 1:323873/1‑56 (MQ=255)
gCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCg < 2:491901/72‑1 (MQ=255)
gCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCg > 1:491901/1‑72 (MQ=255)
gCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGc > 2:499874/1‑90 (MQ=255)
gCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGc > 2:646786/1‑90 (MQ=255)
gCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGc > 1:179421/1‑90 (MQ=255)
cTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGcc < 1:378868/90‑1 (MQ=255)
cGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCgg > 1:691276/1‑90 (MQ=255)
cGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCgg > 2:738966/1‑90 (MQ=255)
gggAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGAt < 1:267331/90‑1 (MQ=255)
gtTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGaa < 2:146932/90‑1 (MQ=255)
ggCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATcc > 1:518545/1‑90 (MQ=255)
cGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCgg < 2:105028/90‑1 (MQ=255)
|
GAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGG > NZ_CP009273/2229869‑2230041
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
GTAATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAAACCATA > NZ_CP009273/2229861‑2230055
|
GTAATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGA > SRR3722073.481386/1‑100 (MQ=60)
GTAATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGA > SRR3722073.542945/1‑100 (MQ=60)
AATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAAC < SRR3722073.282458/100‑1 (MQ=60)
GCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGA > SRR3722073.109554/1‑100 (MQ=60)
TGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGG < SRR3722073.600565/100‑1 (MQ=60)
GGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACtgtctcttatacacatctgacgc > SRR3722073.330751/1‑77 (MQ=60)
GTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCtgtctct > SRR3722073.502325/1‑93 (MQ=60)
GTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGC > SRR3722073.182890/1‑100 (MQ=60)
GTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGG > SRR3722073.705350/1‑100 (MQ=60)
CTCGGGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCT < SRR3722073.386933/100‑1 (MQ=60)
GGGAAGTGAAGTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAA < SRR3722073.272979/100‑1 (MQ=60)
GTTTAAGAAAGGCGAGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCC > SRR3722073.529456/1‑100 (MQ=60)
AGGAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAAACCA > SRR3722073.716038/1‑100 (MQ=60)
GAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAAACCATA > SRR3722073.270297/1‑100 (MQ=60)
|
GTAATACCGAGAAATGTGTGGGTTGTCTGCTTTGTGGTCACGTCTGCCCGGTGGGTTGTATTGAGCTCGGGGAAGTGAAGTTTAAGAAAGGCGAGAAAGAACACCCGGTAACGTTGTAAAACCAGAGACGCATCCGGCATTTGGTTCCTGTCGCCGGATGCGGCTTGAACGCCTTATCCGGCCTACAAAACCATA > NZ_CP009273/2229861‑2230055
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
