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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,896,621 |
A→G |
D147D (GAT→GAC) |
bglB ← |
6‑phospho‑beta‑glucosidase BglB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,896,621 | 0 | A | G | 96.0%
| 65.0
/ ‑3.6
| 25 | D147D (GAT→GAC) | bglB | 6‑phospho‑beta‑glucosidase BglB |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (16/8); total (17/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.26e-01 |
CGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGA > NZ_CP009273/3896534‑3896689
|
cGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTc < 1:522153/90‑1 (MQ=255)
cATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGAt < 2:652295/90‑1 (MQ=255)
ttAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTa > 2:54596/1‑90 (MQ=255)
ttAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTa > 2:249003/1‑90 (MQ=255)
cAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAAcc > 1:66769/1‑90 (MQ=255)
cAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAAcc > 2:386328/1‑90 (MQ=255)
cAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAAcc > 1:450150/1‑90 (MQ=255)
tAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTa > 1:615345/1‑90 (MQ=255)
aTGTTGGTAGGGAGAAAAGGCCGGGGGGGCGTAATGCTGGAAGTGGTCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAg < 1:640324/90‑1 (MQ=255)
aTGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGACGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAg < 1:249003/90‑1 (MQ=255)
gTTGGTAGCGAGTAAAGCCGGTGGGGGGGTAATGCTCGAAGTGGTCGATGCCCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGcc < 1:254883/90‑1 (MQ=255)
gTTGGAAGGGAGAAAAGCCCGGGCGGGCGTAATGCCCGAAGTGGCCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGcc < 1:495203/90‑1 (MQ=255)
ggTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCat > 2:18870/1‑90 (MQ=255)
aaaGCCCGGGGGGGGGTAATGCTGGAAGGGGTGGATGCCCCCTCTTTTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTc < 2:208334/90‑1 (MQ=255)
cGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATg > 2:519891/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:138871/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:141236/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:105354/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:269040/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:332499/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:541818/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:528750/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:604124/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:208334/1‑90 (MQ=255)
gggggCGTAATGCTCGAGGTGGTCGATCCCCGCTCTATTACCCCACCCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGa < 2:269040/88‑1 (MQ=255)
|
CGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGA > NZ_CP009273/3896534‑3896689
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ 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
CGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > NZ_CP009273/3896534‑3896720
|
CGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCT < SRR3722088.528461/100‑1 (MQ=60)
gaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacaGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCC < SRR3722088.86675/41‑1 (MQ=60)
CATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACC > SRR3722088.67466/1‑100 (MQ=60)
CATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACC > SRR3722088.455392/1‑100 (MQ=60)
ACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTA > SRR3722088.622934/1‑100 (MQ=60)
TATGTTGGTAGCGAGAAAAGCCCGGGGGGGCGTAATGCTCGAAGTGGTCGATGCCCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGG < SRR3722088.294081/100‑1 (MQ=60)
ATGTTGGTAGGGAGAAAAGGCCGGGGGGGCGTAATGCTGGAAGTGGTCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGC < SRR3722088.648256/100‑1 (MQ=60)
ATGTTGGTAGCGAGTAAAGCCCGTGCGGGCGTAATGCTCGAAGTGGTCGACGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGC < SRR3722088.251437/100‑1 (MQ=60)
GTTGGTAGCGAGTAAAGCCGGTGGGGGGGTAATGCTCGAAGTGGTCGATGCCCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCAT < SRR3722088.257365/100‑1 (MQ=60)
GTTGGAAGGGAGAAAAGCCCGGGCGGGCGTAATGCCCGAAGTGGCCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCAT < SRR3722088.501125/100‑1 (MQ=59)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCtgtctcttatac > SRR3722088.485179/1‑88 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722088.106434/1‑100 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722088.535161/1‑100 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722088.548422/1‑100 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722088.271640/1‑100 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722088.210413/1‑100 (MQ=60)
GCGGGCTTAATGCTGGAAGTGGTCGATGCCCGCCCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACC < SRR3722088.500637/100‑1 (MQ=60)
AAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCG > SRR3722088.479721/1‑100 (MQ=60)
GTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCctgtctcttatacacatctccgagcccacgagaccgtactagatc > SRR3722088.286199/1‑55 (MQ=60)
|
CGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > NZ_CP009273/3896534‑3896720
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
