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 |
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 | 88.0%
| 49.7
/ 1.2
| 25 | D147D (GAT→GAC) | bglB | 6‑phospho‑beta‑glucosidase BglB |
| Reads supporting (aligned to +/- strand): ref base A (2/1); new base G (14/8); total (16/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.41e-01 |
ATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGC > NZ_CP009273/3896538‑3896702
|
aTGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATg > 1:823186/1‑90 (MQ=255)
tGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGa > 1:507785/1‑90 (MQ=255)
aTTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCt < 1:825822/90‑1 (MQ=255)
aCTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTc > 1:308095/1‑90 (MQ=255)
tttGTTGGTGGCGAAAAAAGCCCGGGGGGGCGTAATGCTCGAAGGGGTCGATGCCCCCTCGATTACCCCACCCGCCGTAGTTTTTCACCa < 2:280019/88‑1 (MQ=255)
tATGTTGGTAGCGAGAAAAGCCCGTGCGGGCGTAATGCTCGAAGTGGTCGATGCCCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCa < 1:230379/90‑1 (MQ=255)
aTGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAg > 2:545594/1‑90 (MQ=255)
ggTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCat > 2:78876/1‑90 (MQ=255)
ggTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCat > 1:362832/1‑90 (MQ=255)
aGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATg > 2:382378/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:552088/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:733175/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:778404/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:58084/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:470903/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:364104/1‑90 (MQ=255)
gggggCGAAATGCTCGAAGTGGTCGATGCCCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGa < 1:5570/88‑1 (MQ=255)
gggggCGAAATCCTCGAAGTGGTCGAGGCCCGCTCAATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGa < 1:798195/88‑1 (MQ=255)
gCGGGCGTAATGCTGGAGGGGGCCGATGCCCGCCCTATTACCCCACCCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGa < 2:788683/90‑1 (MQ=255)
gtgCGTAATGCTCGGCGTGGGCGATCCCCCCTGGATCACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATa < 2:733175/88‑1 (MQ=255)
gggCGTAATGCTCGAAGTGATCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATa < 1:194602/90‑1 (MQ=255)
gggCGAAATGCGGGAGGTGGTGGTTGCCCGCTCGATTAGCCCACCCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATa < 1:433762/90‑1 (MQ=255)
gCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAAc > 2:683577/1‑90 (MQ=255)
aTGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTAc > 2:95730/1‑90 (MQ=255)
tCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGc > 2:746954/1‑90 (MQ=255)
|
ATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGC > NZ_CP009273/3896538‑3896702
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTGTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > NZ_CP009273/3896528‑3896720
|
GTGTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATG > SRR3722079.832000/1‑100 (MQ=60)
TGTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGA > SRR3722079.512394/1‑100 (MQ=60)
ctctctggtctcgtgggctcggagatgtgtataagagacagACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGAC < SRR3722079.564711/59‑1 (MQ=60)
ATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCTC < SRR3722079.834661/100‑1 (MQ=60)
CCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTC > SRR3722079.310601/1‑100 (MQ=60)
cccgttttattttggtagagagaaaaccccgtgggggtgtattgcgCGAAGTGGTCGATGCCCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCC < SRR3722079.178669/54‑1 (MQ=60)
ACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCAT > SRR3722079.365669/1‑100 (MQ=60)
TATGTTGGTAGCGAGAAAAGCCCGTGCGGGCGTAATGCTCGAAGTGGTCGATGCCCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGG < SRR3722079.232337/100‑1 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCtgtctcttatacacatctccgagcccacgagaccagagaggatctcgtatgccgtct > SRR3722079.300524/1‑43 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCActgtctcttat > SRR3722079.773350/1‑89 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722079.786746/1‑100 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722079.475021/1‑100 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722079.741017/1‑100 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722079.557384/1‑100 (MQ=60)
GGGGGCGAAATGCTCGAAGTGGTCGATGCCCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACC < SRR3722079.5620/100‑1 (MQ=60)
GGGGGCGAAATCCTCGAAGTGGTCGAGGCCCGCTCAATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACC < SRR3722079.806747/100‑1 (MQ=60)
GGGCGTAATGCTCGAAGTGATCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAG < SRR3722079.196285/100‑1 (MQ=60)
GTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > SRR3722079.600602/1‑100 (MQ=60)
GTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > SRR3722079.5101/1‑100 (MQ=60)
GTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > SRR3722079.439007/1‑100 (MQ=60)
GTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > SRR3722079.421089/1‑100 (MQ=60)
GTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > SRR3722079.343727/1‑100 (MQ=60)
|
GTGTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > NZ_CP009273/3896528‑3896720
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
