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 I75 R1
|
71 |
32.8 |
2150506 |
93.3% |
2006422 |
83.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,620,259 |
A→T |
D880E (GAT→GAA) |
rbbA ← |
ribosome‑associated ATPase/putative transporter RbbA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,620,259 | 0 | A | T | 100.0%
| 121.9
/ NA
| 46 | D880E (GAT→GAA) | rbbA | ribosome‑associated ATPase/putative transporter RbbA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (26/20); total (26/20) |
TTTTTTCAGCAGCAGGATACTTAAGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGATCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCAACGTCCAGGCC > NZ_CP009273/3620175‑3620341
|
ttttttCAGCAGCAGGATACTTAAGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAg < 1:869582/90‑1 (MQ=255)
tttttCAGCAGCAGGATACTTAAGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAgc < 1:183362/90‑1 (MQ=255)
agGATACTTAAGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAAc < 2:930863/90‑1 (MQ=255)
aTACTTAAGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTc > 1:945062/1‑90 (MQ=255)
tACTTAAGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTcc < 2:345314/90‑1 (MQ=255)
aCTTAAGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTccc > 2:582731/1‑90 (MQ=255)
tAAGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCcgcg > 2:987179/1‑90 (MQ=255)
tAAGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCcgcg > 2:341353/1‑90 (MQ=255)
tAAGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCcgcg < 1:858203/90‑1 (MQ=255)
aaGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCgg > 2:386686/1‑90 (MQ=255)
cccATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCg > 1:60455/1‑90 (MQ=255)
ccATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGa > 1:50794/1‑90 (MQ=255)
cATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGAt < 1:582731/90‑1 (MQ=255)
cATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGAt > 2:594416/1‑90 (MQ=255)
cATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGAGGGCGAt > 1:19781/1‑90 (MQ=255)
aTCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGAt < 2:976871/89‑1 (MQ=255)
aTCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGAt > 1:976871/1‑89 (MQ=255)
tCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAg > 1:994680/1‑90 (MQ=255)
cAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAg > 2:394044/1‑90 (MQ=255)
cAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGACAg > 2:742488/1‑90 (MQ=255)
cAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGAGGGCGATAGTCAg < 2:19781/90‑1 (MQ=255)
aGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGa < 2:952740/90‑1 (MQ=255)
aTGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGa < 1:723649/90‑1 (MQ=255)
ggCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTTAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACt > 1:556909/1‑90 (MQ=255)
ggCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACt < 2:716018/90‑1 (MQ=255)
cTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTgg < 2:60455/90‑1 (MQ=255)
tATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGt > 1:6552/1‑90 (MQ=255)
aaCGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAgc > 2:325574/1‑39 (MQ=255)
aaCGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAgc < 1:325574/39‑1 (MQ=39)
aaCGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTaa > 2:683003/1‑90 (MQ=255)
aCGGGATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCggggtaa > 2:885544/1‑86 (MQ=255)
ggATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCt > 1:941281/1‑90 (MQ=255)
ggATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCt > 2:977812/1‑90 (MQ=255)
gATAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTc > 1:364925/1‑90 (MQ=255)
aTAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCg > 1:1030698/1‑90 (MQ=255)
aTAAAAAGTTGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCg > 1:158419/1‑90 (MQ=255)
ttGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCa > 2:1013658/1‑90 (MQ=255)
ttGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCa < 1:266332/90‑1 (MQ=255)
tGCCACAAATCAGTTAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCaa < 2:556909/90‑1 (MQ=255)
tGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCaa < 2:667306/90‑1 (MQ=255)
tGCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCaa < 1:1011043/90‑1 (MQ=255)
ggtcacaAAGCAGGCAGTTCCGGCGCTTTCCGGGACGACCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAGCCTCGCCGAACCaa < 2:121804/87‑1 (MQ=255)
gCCACAAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCAAc < 1:394044/90‑1 (MQ=255)
cacaAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCAACGt > 2:607577/1‑90 (MQ=255)
caAATCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCAACGTcc < 2:790818/90‑1 (MQ=255)
aTCAGTCAGTTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCAACGTCCAgg > 2:161545/1‑90 (MQ=255)
cagtcagtTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCAACGTCCAGGcc < 2:253930/90‑1 (MQ=255)
cagtcagtTCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCAACGTCCAGGcc < 2:994680/90‑1 (MQ=255)
|
TTTTTTCAGCAGCAGGATACTTAAGCCCATCACCAGCGGGATGGCTATCAGTAACGGGATAAAAAGTTGCCACAAATCAGTCAGATCCAGCGCTTTCGAGAACGTCCCGCGGGCGATAGTCAGAAAATGACTGGTCGGGTAAACCTCGCCGATCCAACGTCCAGGCC > NZ_CP009273/3620175‑3620341
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ 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
ATCGAGAAGAATCGCCGCATTTTGCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCATCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTATCGAC > NZ_CP009273/3736726‑3736911
|
ATCGAGAAGAATCGCCGCATTTTGCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGT > SRR3722213.213487/1‑100 (MQ=60)
TCGCCGCATTTTGCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAA > SRR3722213.638327/1‑100 (MQ=60)
ATTTTGCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCC < SRR3722213.1007844/100‑1 (MQ=60)
aataacgggtctcgtgggctcggagatgtgtataagagacagGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGAC < SRR3722213.994502/58‑1 (MQ=60)
aataacgggtctcgtgggctcggagatgtgtataagagacagGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACACAGGAC < SRR3722213.887543/58‑1 (MQ=60)
GCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGAC > SRR3722213.377543/1‑100 (MQ=60)
tacgagataataacgggtctcgtgggctcggagatgtgtataagagacaGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAAC < SRR3722213.930141/51‑1 (MQ=60)
GATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAAC < SRR3722213.609316/100‑1 (MQ=60)
gtgtataagagacAGGTTCTGTCATGTCGATTGTGCTGGATATGATCGCTACACTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAG < SRR3722213.214908/87‑1 (MQ=60)
ACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGA > SRR3722213.355318/1‑100 (MQ=60)
AGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCATCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGC < SRR3722213.1083739/100‑1 (MQ=60)
GGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACtgtctcttat > SRR3722213.1003163/1‑90 (MQ=60)
GTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCAT > SRR3722213.94331/1‑100 (MQ=60)
GTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCAT > SRR3722213.515549/1‑100 (MQ=60)
GTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCAT > SRR3722213.827649/1‑100 (MQ=60)
GTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCtgtctcttatacacatctccgagcccacgag > SRR3722213.221964/1‑69 (MQ=60)
GTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTG > SRR3722213.372817/1‑100 (MQ=60)
GTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTG > SRR3722213.969666/1‑100 (MQ=60)
GGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATT > SRR3722213.615306/1‑100 (MQ=60)
GGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATT > SRR3722213.257132/1‑100 (MQ=60)
CTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACctgtctcttatacacatctccgagccca > SRR3722213.714208/1‑72 (MQ=60)
CTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAA > SRR3722213.635272/1‑100 (MQ=60)
CTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAA > SRR3722213.405002/1‑100 (MQ=60)
CTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAA > SRR3722213.995015/1‑100 (MQ=60)
CTACTCTCCTTTCCGAAGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAA > SRR3722213.588144/1‑100 (MQ=60)
ACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAAGC < SRR3722213.980135/100‑1 (MQ=60)
CTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTA < SRR3722213.385144/100‑1 (MQ=60)
CCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCtgtctcttatacacatctccga > SRR3722213.997669/1‑78 (MQ=60)
TTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTATCGAC < SRR3722213.624558/100‑1 (MQ=60)
TTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTATCGAC < SRR3722213.1027312/100‑1 (MQ=60)
|
ATCGAGAAGAATCGCCGCATTTTGCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCATCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTATCGAC > NZ_CP009273/3736726‑3736911
|
| 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: ‑ |
