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 |
1,848,011 |
T→C |
T76A (ACT→GCT) |
ydjE ← |
MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,848,011 | 0 | T | C | 85.7%
| 41.5
/ 2.8
| 21 | T76A (ACT→GCT) | ydjE | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base T (3/0); new base C (8/10); total (11/10) |
| Fisher's exact test for biased strand distribution p-value = 2.14e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.72e-01 |
CAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCA > NZ_CP009273/1847939‑1848094
|
caATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAAt > 1:539794/1‑90 (MQ=255)
aaTACCGACGATGGGAAGCTTTATGCGAAACCCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATa > 2:746097/1‑90 (MQ=255)
aaTACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATa > 2:496405/1‑90 (MQ=255)
aTACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATaa > 2:378795/1‑90 (MQ=255)
cgacgaTGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCaa < 1:685883/90‑1 (MQ=255)
gacgaTGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCaaa > 1:446916/1‑90 (MQ=255)
agaagaTTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAAt < 1:773302/90‑1 (MQ=255)
aTGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTa > 2:758561/1‑90 (MQ=255)
aaaCGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTTATGCCGAGGTAAAggc > 1:284144/1‑90 (MQ=255)
aaaCGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAggc > 2:23083/1‑90 (MQ=255)
ccTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCAtt < 1:758651/90‑1 (MQ=255)
tGCGCCGCCCAAAGTAGTCACCAATAGACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGa < 2:465719/90‑1 (MQ=255)
tGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGa < 2:721449/90‑1 (MQ=255)
ccgccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGaa < 1:558224/90‑1 (MQ=255)
ccgccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGaa < 2:739758/90‑1 (MQ=255)
gccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAat > 1:804143/1‑90 (MQ=255)
tagtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAc < 1:550684/90‑1 (MQ=255)
tagtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAc < 1:278434/90‑1 (MQ=255)
gtCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAcca > 2:365245/1‑90 (MQ=255)
ccaccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTAcc < 1:298871/90‑1 (MQ=255)
caccaGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCa > 1:418415/1‑90 (MQ=255)
|
CAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCA > NZ_CP009273/1847939‑1848094
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ 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
GGACAAAAGCGGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTA > NZ_CP009273/1847915‑1848103
|
GGACAAAAGCGGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAG < SRR3722079.272256/100‑1 (MQ=60)
GAGCGGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCC < SRR3722079.592798/100‑1 (MQ=60)
CCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAAT > SRR3722079.544893/1‑100 (MQ=60)
CAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAA > SRR3722079.450821/1‑100 (MQ=60)
CGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGC < SRR3722079.693090/100‑1 (MQ=60)
AGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAA < SRR3722079.781587/100‑1 (MQ=60)
GATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTTATGCCGAGGTAAAGGC > SRR3722079.286499/1‑100 (MQ=60)
GCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAAT > SRR3722079.812768/1‑100 (MQ=60)
CCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTA < SRR3722079.766768/100‑1 (MQ=60)
CCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAC < SRR3722079.563626/100‑1 (MQ=60)
TAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGC < SRR3722079.280757/100‑1 (MQ=60)
TAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGC < SRR3722079.555959/100‑1 (MQ=60)
CCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCA > SRR3722079.422021/1‑100 (MQ=60)
CCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTA < SRR3722079.301321/100‑1 (MQ=60)
|
GGACAAAAGCGGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTA > NZ_CP009273/1847915‑1848103
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
