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 F1 I178 R2
|
5 |
19.9 |
1206538 |
94.7% |
1142591 |
84.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| MC JC |
NZ_CP009273 |
2,399,465 |
Δ7 bp |
coding (650‑656/939 nt) |
lrhA ← |
transcriptional regulator LrhA |
|
| | | | seq id |
start |
end |
size |
←reads |
reads→ |
gene |
description |
|---|
| * |
* |
÷ |
NZ_CP009273 |
2399465 |
2399471 |
7 |
18 [0] |
[0] 18 |
lrhA |
transcriptional regulator LrhA |
|
| |
seq id |
position |
reads (cov) |
reads (cov) |
score |
skew |
freq |
annotation |
gene |
product |
| * |
? |
NZ_CP009273 |
= 2399464 | 0 (0.000) | 18 (0.890) |
13/166 |
0.4 |
100% |
coding (657/939 nt) |
lrhA |
transcriptional regulator LrhA |
| ? | NZ_CP009273 |
2399472 = |
0 (0.000) | coding (649/939 nt) |
lrhA |
transcriptional regulator LrhA |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAG > NZ_CP009273/2399377‑2399558
|
ACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCC > SRR3722051.299873/1‑100 (MQ=60)
CATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAAAATCTGCTT > SRR3722051.200069/1‑100 (MQ=60)
CATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTAT > SRR3722051.456390/1‑100 (MQ=60)
TCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTA < SRR3722051.274144/100‑1 (MQ=60)
GCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCAC < SRR3722051.234804/100‑1 (MQ=60)
CGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCG > SRR3722051.487561/1‑100 (MQ=60)
CACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGAT < SRR3722051.574445/100‑1 (MQ=60)
CGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAG < SRR3722051.436049/100‑1 (MQ=60)
|
ACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAG > NZ_CP009273/2399377‑2399558
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
