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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
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%
| 25.8
/ NA
| 9 | E232G (GAA→GGA) | torC | pentaheme c‑type cytochrome TorC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (6/3); total (6/3) |
GTGACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGT > NZ_CP009273/1054147‑1054307
|
gtgACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAg > 2:27044/1‑90 (MQ=255)
tctATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAg < 1:404631/82‑1 (MQ=255)
tctATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAg > 2:404631/1‑82 (MQ=255)
tATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACg < 1:414811/90‑1 (MQ=255)
gCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGaa > 1:333355/1‑90 (MQ=255)
gTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCg < 1:444147/90‑1 (MQ=255)
tctGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACg > 2:50636/1‑90 (MQ=255)
ctgctgCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGt > 1:311401/1‑90 (MQ=255)
ctgctgCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGt > 2:172368/1‑90 (MQ=255)
|
GTGACACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGT > NZ_CP009273/1054147‑1054307
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCG > NZ_CP009273/1054153‑1054312
|
CGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACG < SRR3722087.409325/100‑1 (MQ=60)
TATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGAC < SRR3722087.419645/100‑1 (MQ=60)
CGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAA > SRR3722087.337033/1‑100 (MQ=60)
CTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGT > SRR3722087.314685/1‑100 (MQ=60)
GTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCG < SRR3722087.449338/100‑1 (MQ=60)
|
CGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCG > NZ_CP009273/1054153‑1054312
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
