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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
991,969 |
T→G |
L144F (TTA→TTC) |
ssuA ← |
aliphatic sulfonate ABC transporter substrate‑binding protein SsuA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 991,969 | 0 | T | G | 100.0%
| 27.9
/ NA
| 10 | L144F (TTA→TTC) | ssuA | aliphatic sulfonate ABC transporter substrate‑binding protein SsuA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (5/5); total (5/5) |
TGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGTAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTT > NZ_CP009273/991925‑992050
|
tGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGa < 2:278310/90‑1 (MQ=255)
tGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGa < 2:70092/90‑1 (MQ=255)
aaaCTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATc > 1:242597/1‑90 (MQ=255)
aaaCTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATc > 2:498635/1‑90 (MQ=255)
aaGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTAc < 2:206033/90‑1 (MQ=255)
ggCCTGACGCAGTGCACGCAGGAAAAGGTtgtgtg > 1:118470/1‑35 (MQ=38)
ggCCTGACGCAGTGCACGCAGGAAAAGGTtgtgtg < 2:118470/35‑1 (MQ=38)
gCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGc < 1:102017/90‑1 (MQ=255)
gCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGttt > 2:318281/1‑90 (MQ=255)
gCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGttt > 2:552168/1‑90 (MQ=255)
|
TGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGTAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTT > NZ_CP009273/991925‑992050
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
CCTTGCTGGAACGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGTAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTTTCTGC > NZ_CP009273/991877‑992055
|
CCTTGCTGGAACGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGTAAAAGGT < SRR3722111.363288/100‑1 (MQ=60)
GTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgta > SRR3722111.250121/1‑54 (MQ=60)
GTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgta > SRR3722111.559024/1‑54 (MQ=60)
GGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATC > SRR3722111.245475/1‑100 (MQ=60)
ACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgt > SRR3722111.119961/1‑55 (MQ=60)
GCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTTTCTGC < SRR3722111.103292/100‑1 (MQ=60)
|
CCTTGCTGGAACGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGTAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTTTCTGC > NZ_CP009273/991877‑992055
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
