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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,054,234 |
A→G |
E232G (GAA→GGA) |
torC → |
pentaheme c‑type cytochrome TorC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,054,234 | 0 | A | G | 100.0%
| 26.1
/ NA
| 10 | E232G (GAA→GGA) | torC | pentaheme c‑type cytochrome TorC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (7/3); total (7/3) |
GACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTC > NZ_CP009273/1054149‑1054319
|
gACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTg > 1:80250/1‑90 (MQ=255)
gTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCt > 1:42533/1‑90 (MQ=255)
gATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGAc > 2:205117/1‑90 (MQ=255)
gATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGAc < 2:65007/90‑1 (MQ=255)
gATATTAAGCCAATTGATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCGGCTTCGGGAGTGAAAGTCCTTAAACGTGAc > 2:26241/1‑90 (MQ=255)
tatTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACgg > 1:286803/1‑90 (MQ=255)
tatTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACgg > 2:519271/1‑90 (MQ=255)
gcgAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGGGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATGGaa > 2:304471/1‑90 (MQ=255)
ctgctgCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGt < 1:61471/90‑1 (MQ=255)
tCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTc < 2:286803/90‑1 (MQ=255)
|
GACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTC > NZ_CP009273/1054149‑1054319
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TGACAGTGGTGACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTAC > NZ_CP009273/1054139‑1054317
|
TGACAGTGGTGACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTG > SRR3722114.81097/1‑100 (MQ=60)
GTGACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCT > SRR3722114.42944/1‑100 (MQ=60)
ACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGG > SRR3722114.289831/1‑100 (MQ=60)
CTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTAC < SRR3722114.62084/100‑1 (MQ=60)
|
TGACAGTGGTGACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTAC > NZ_CP009273/1054139‑1054317
|
| 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: ‑ |
