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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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 | 100.0%
| 68.7
/ NA
| 21 | T76A (ACT→GCT) | ydjE | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/9); total (12/9) |
TACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCA > NZ_CP009273/1847942‑1848094
|
tACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAAc > 1:720956/1‑90 (MQ=255)
aCCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAAcc > 1:209396/1‑90 (MQ=255)
cgacgaTGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCaa < 1:739074/90‑1 (MQ=255)
cgaTGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACa > 1:324884/1‑90 (MQ=255)
agaTTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGcc < 2:610388/90‑1 (MQ=255)
agaTTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGcc < 2:324884/90‑1 (MQ=255)
gaTTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCg < 1:343123/90‑1 (MQ=255)
ttATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAgg > 2:83075/1‑90 (MQ=255)
gAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGAAAAgg > 1:571680/1‑90 (MQ=255)
aaaCGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAggc > 2:702558/1‑90 (MQ=255)
tGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGa > 1:309386/1‑90 (MQ=255)
tGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGa > 2:387518/1‑90 (MQ=255)
ccgccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGaa < 1:651417/90‑1 (MQ=255)
ccgccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGaa < 1:330881/90‑1 (MQ=255)
ccgccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGaa < 1:177426/90‑1 (MQ=255)
gccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAat > 2:579005/1‑90 (MQ=255)
aaGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTAttt > 1:587083/1‑90 (MQ=255)
aaTAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCAtt < 2:199226/90‑1 (MQ=255)
aaaCCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCg < 2:199595/47‑1 (MQ=255)
aaaCCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCg > 1:199595/1‑47 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCa > 2:738560/1‑90 (MQ=255)
|
TACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCA > NZ_CP009273/1847942‑1848094
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ 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
ACAAAAGCGGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTAA > NZ_CP009273/1847917‑1848104
|
ACAAAAGCGGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTG < SRR3722073.45635/100‑1 (MQ=60)
ACAAAAGCGGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTG < SRR3722073.465845/100‑1 (MQ=60)
AAAGCGGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGC < SRR3722073.533657/100‑1 (MQ=60)
GTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAAC > SRR3722073.735519/1‑100 (MQ=60)
TTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACC > SRR3722073.213686/1‑100 (MQ=60)
GCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACA > SRR3722073.331783/1‑100 (MQ=60)
CGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGC < SRR3722073.754040/100‑1 (MQ=60)
AGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGAAAAGG > SRR3722073.583620/1‑100 (MQ=60)
GATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGC < SRR3722073.350392/100‑1 (MQ=60)
CGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGA > SRR3722073.315943/1‑100 (MQ=60)
GCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTT > SRR3722073.599353/1‑100 (MQ=60)
CCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAC < SRR3722073.180877/100‑1 (MQ=60)
CCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAC < SRR3722073.337916/100‑1 (MQ=60)
CCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAC < SRR3722073.664806/100‑1 (MQ=60)
AGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCctgtctcttatacacatctgacgctgccgacga > SRR3722073.203617/1‑67 (MQ=60)
CACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTAA > SRR3722073.383996/1‑100 (MQ=60)
|
ACAAAAGCGGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTAA > NZ_CP009273/1847917‑1848104
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
