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 F3 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
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 | 100.0%
| 128.9
/ NA
| 42 | D147D (GAT→GAC) | bglB | 6‑phospho‑beta‑glucosidase BglB |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (28/14); total (28/14) |
TGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTT > NZ_CP009273/3896539‑3896707
|
tGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGa > 1:234624/1‑90 (MQ=255)
gATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGc < 1:120793/90‑1 (MQ=255)
gATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGc < 2:801111/90‑1 (MQ=255)
gATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGc < 2:589552/90‑1 (MQ=255)
tCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGa > 1:294808/1‑90 (MQ=255)
tAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTa > 1:227639/1‑90 (MQ=255)
cACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGttttt > 2:286531/1‑90 (MQ=255)
cACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGttttt > 1:384861/1‑90 (MQ=255)
ggtgggTGGCGAGAAAAGCCGGGGGGGGCGTAATGCTCGAGGGGGTCGAGGCCCGCTCGTTTACCCCAACCGCCGTAGTTTTTCACCAGc < 1:635992/86‑1 (MQ=255)
tttGGTAGCGAGAAAAGCCCGGGGGGGCGAAATGCTCGAGGTGGTCGATGCCCGCTCGATTACCCAAACCGCCGTAGTTTTTCACCAGcc < 2:575199/89‑1 (MQ=255)
gTTGGTAGCGAGAAAAGCCCGGGGGGGCGTAATGCTCGAAGTGGTCGATGCCCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGcc < 2:167352/90‑1 (MQ=255)
ggTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCat > 2:618449/1‑90 (MQ=255)
ggTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCat > 1:354227/1‑90 (MQ=255)
ggTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCat > 1:244776/1‑90 (MQ=255)
gTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCata > 1:468421/1‑90 (MQ=255)
gTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCata > 2:508983/1‑90 (MQ=255)
tAGCGAGAAAAGCCCGTGGGGGCGAAATGCTAGAAGTGGTCGATGCCCCCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCatat < 2:777326/90‑1 (MQ=255)
aGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATg > 2:767716/1‑90 (MQ=255)
cGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGc > 2:352979/1‑90 (MQ=255)
aGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCAt > 1:795645/1‑90 (MQ=255)
gTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCAtt > 2:288741/1‑90 (MQ=255)
cccGGGCGGGTTTATTGCTGGAAGTGGTCGTTGCCCCCTCGATTACCCCACCCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTaa < 2:354489/89‑1 (MQ=255)
cccGGGCGGGCGTAATCCTCGAAGGGGTCGATGCCCCCTCGATTACCCCACCCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTaa < 1:945854/89‑1 (MQ=255)
cGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATg > 1:956728/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:343383/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:506970/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:517859/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:802394/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:487755/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:736249/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:290783/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:541960/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 1:664881/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:1000434/1‑90 (MQ=255)
gTGCGGGCGTAATGCTCGAAGTGGTCGATAACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATgg > 2:781288/1‑90 (MQ=255)
tGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATggg > 1:466351/1‑90 (MQ=255)
gggCGTATTGCTCGAGGTGGTCGATGACCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATa < 2:227639/90‑1 (MQ=255)
gggCGTAATGCTCGAAGTGGTCGATGCCCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATa < 2:403420/90‑1 (MQ=255)
gggCGTAATGCCCGAAGTGGTCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATa < 2:12927/90‑1 (MQ=255)
aaGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGc > 1:181476/1‑90 (MQ=255)
gTGGTCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCtt < 2:908727/90‑1 (MQ=255)
gTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCtt < 2:506970/90‑1 (MQ=255)
|
TGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTT > NZ_CP009273/3896539‑3896707
|
| 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
TGTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > NZ_CP009273/3896529‑3896720
|
TGTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGA > SRR3722236.238112/1‑100 (MQ=60)
GTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGAC < SRR3722236.689604/100‑1 (MQ=60)
CATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGA > SRR3722236.299074/1‑100 (MQ=60)
GATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCC < SRR3722236.122491/100‑1 (MQ=60)
CATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCtgtctcttatacacatc > SRR3722236.162098/1‑83 (MQ=60)
ACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTA > SRR3722236.231023/1‑100 (MQ=60)
GCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTT > SRR3722236.390260/1‑100 (MQ=60)
aagccttcgtcggcggcgtcagatttgtaaaagagacgGGGCGTAATGCTCGAGGTGGTCGATGCCCGCTCGATTACCCCAACCGCCGTAGTTTTTCACC < SRR3722236.317017/62‑1 (MQ=56)
ACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCAT > SRR3722236.248420/1‑100 (MQ=60)
ACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCAT > SRR3722236.359254/1‑100 (MQ=60)
CTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATA > SRR3722236.475340/1‑100 (MQ=60)
ggtgggtggcgagaaaagccgggggGGGCGTAATGCTCGAGGGGGTCGAGGCCCGCTCGTTTACCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCA < SRR3722236.646377/75‑1 (MQ=41)
GTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCAT > SRR3722236.809455/1‑100 (MQ=60)
GAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATG > SRR3722236.973604/1‑100 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATctgtctctta > SRR3722236.108970/1‑90 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722236.514648/1‑100 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722236.550300/1‑100 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722236.675916/1‑100 (MQ=60)
AGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGG > SRR3722236.748807/1‑100 (MQ=60)
GTAAAGACCGTGCGGGCGTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGG > SRR3722236.473219/1‑100 (MQ=60)
cccggGCGGGCGTAATCCTCGAAGGGGTCGATGCCCCCTCGATTACCCCACCCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACG < SRR3722236.962542/95‑1 (MQ=60)
GTAATGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGC > SRR3722236.184161/1‑100 (MQ=60)
TGCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGA > SRR3722236.771487/1‑100 (MQ=60)
GCTCGAAGTGGTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGAT > SRR3722236.388527/1‑100 (MQ=60)
GTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > SRR3722236.372817/1‑100 (MQ=60)
GTCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > SRR3722236.809200/1‑100 (MQ=60)
|
TGTAACGACATGTTGATTTCATTAAACGTCAGCCATAACGCCACTTTATGTTGGTAGCGAGTAAAGACCGTGCGGGCGTAATGCTCGAAGTGATCGATGACCGCTCGATTAGCCCAACCGCCGTAGTTTTTCACCAGCCCATATGGCATTTCGTAATGGGATAACGTTACCAGCGGCTTGATCCCCGCCTGC > NZ_CP009273/3896529‑3896720
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
