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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 76.7%
| 43.1
/ 16.8
| 30 | E232G (GAA→GGA) | torC | pentaheme c‑type cytochrome TorC |
| Reads supporting (aligned to +/- strand): ref base A (5/2); new base G (16/7); total (21/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.33e-01 |
ACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCA > NZ_CP009273/1054152‑1054320
|
acGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGaaa < 2:776267/90‑1 (MQ=255)
cTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTc > 2:822906/1‑90 (MQ=255)
cTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTc > 2:468948/1‑90 (MQ=255)
cTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTc > 2:306382/1‑90 (MQ=255)
tGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTcc > 2:105941/1‑90 (MQ=255)
tctATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTaaa > 1:825526/1‑90 (MQ=255)
tATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACg > 2:612998/1‑90 (MQ=255)
ttGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTg > 1:201698/1‑90 (MQ=255)
gATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGAc > 2:674855/1‑90 (MQ=255)
gATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGAc > 2:531738/1‑90 (MQ=255)
gATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGAc > 2:116815/1‑90 (MQ=255)
gATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGAc > 2:829410/1‑90 (MQ=255)
gATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGAc > 2:648008/1‑90 (MQ=255)
tAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGa > 2:568124/1‑90 (MQ=255)
aaTTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCt > 2:713778/1‑90 (MQ=255)
aaTTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCt > 1:231909/1‑90 (MQ=255)
aTTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTg > 2:497847/1‑90 (MQ=255)
gcggcgAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAAtt > 2:667250/1‑90 (MQ=255)
ggcgAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGa < 1:829410/90‑1 (MQ=255)
aagCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGGGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACgg > 2:614689/1‑90 (MQ=255)
ctctGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAg > 1:408002/1‑90 (MQ=255)
ctctGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGAc > 1:540886/1‑90 (MQ=255)
ctgctgCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGt < 2:336144/90‑1 (MQ=255)
gctgcCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCa < 1:94924/90‑1 (MQ=255)
tgcctgcTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGc > 1:755326/1‑90 (MQ=255)
gcctgcTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCg < 1:568124/90‑1 (MQ=255)
ttCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACt < 2:64276/90‑1 (MQ=255)
tCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTc < 1:713778/90‑1 (MQ=255)
tCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGACAGCGTGTACTc < 1:328824/90‑1 (MQ=255)
cGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCa < 2:540886/90‑1 (MQ=255)
|
ACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCA > NZ_CP009273/1054152‑1054320
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
CACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCACCCAATTCCCAGG > NZ_CP009273/1054151‑1054333
|
CACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAA > SRR3722079.834363/1‑100 (MQ=60)
CTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTG > SRR3722079.203439/1‑100 (MQ=60)
ATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCT > SRR3722079.233876/1‑100 (MQ=60)
GGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGC < SRR3722079.838288/100‑1 (MQ=60)
ATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAG > SRR3722079.411475/1‑100 (MQ=60)
GCCTCTGGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGAC > SRR3722079.546008/1‑100 (MQ=60)
GGTTCTCTGCTGCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGC > SRR3722079.763401/1‑100 (MQ=60)
GCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTC < SRR3722079.95669/100‑1 (MQ=60)
GCCTGCTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCACC < SRR3722079.573695/100‑1 (MQ=60)
CTTCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCACCCAATT > SRR3722079.104624/1‑100 (MQ=60)
TCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCACCCAATTCC < SRR3722079.721379/100‑1 (MQ=60)
TCGGGAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGACAGCGTGTACTCACCCAATTCC < SRR3722079.331454/100‑1 (MQ=60)
GAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCACCCAATTCCCAGG < SRR3722079.762147/100‑1 (MQ=60)
|
CACGCTGTACTCTATTGATATTAAGCCAATTTATGCGGCGAAAGGCGATAAAGAAGCCTCTGGTTCTCTGCTGCCTGCTTCGGAAGTGAAAGTCCTTAAACGTGACGGCGACTGGCTGCAAATTGAAATTACCGGCTGGACGGAAAGCGCCGGACGTCAGCGTGTACTCACCCAATTCCCAGG > NZ_CP009273/1054151‑1054333
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
