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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
701,647 |
G→A |
P33P (CCG→CCA) |
glnS → |
glutamine‑‑tRNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 701,647 | 0 | G | A | 97.4%
| 136.5
/ ‑4.0
| 39 | P33P (CCG→CCA) | glnS | glutamine‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (22/16); total (22/17) |
| Fisher's exact test for biased strand distribution p-value = 4.36e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.20e-01 |
GAAGCCCGCCCGACTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCGCCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCC > NZ_CP009273/701561‑701729
|
gAAGCCCGCCCGACGAACTTTATCCGTCAGATCAGCGATTAAGATCTGTCCAGTGGTAAGCACACCACAGTACACACCCGTTTCccaccg > 2:80570/1‑90 (MQ=255)
aaGCCCGCCCGACTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCGCCgg < 2:656124/90‑1 (MQ=255)
ccgcccgACTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGcc > 2:867314/1‑90 (MQ=255)
cTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACCCCACAGTACACCCCCGTTTCCCACCGGAGCCGAATGGCt < 1:80570/90‑1 (MQ=255)
aCTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATc < 1:48155/90‑1 (MQ=255)
aCTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATc < 1:650306/90‑1 (MQ=255)
cTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCt < 2:91243/90‑1 (MQ=255)
cTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCt < 2:728480/90‑1 (MQ=255)
cTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCt < 1:395102/90‑1 (MQ=255)
gTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTg > 1:852091/1‑90 (MQ=255)
tCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTgg > 2:595315/1‑90 (MQ=255)
tCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTgg > 2:210906/1‑90 (MQ=255)
cAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGc > 1:186447/1‑90 (MQ=255)
catcGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGc < 1:656038/90‑1 (MQ=255)
atcGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGcc > 1:704373/1‑85 (MQ=255)
atcGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGcc < 2:704373/85‑1 (MQ=255)
tcGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGa > 2:873300/1‑90 (MQ=255)
ggCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCt > 1:458672/1‑90 (MQ=255)
ccAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGa < 2:19549/90‑1 (MQ=255)
gTGGTAAGCACACCACAGTACACACCCGTTTCCGACCGGAGCCGAATGGCTATCTGCATATTGGCAATGCGAAATCTATCTGCCTGAACt > 2:202693/1‑90 (MQ=255)
aaGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCggg > 2:910064/1‑90 (MQ=255)
caccacAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGc > 2:265919/1‑90 (MQ=255)
caccacAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGc > 1:376369/1‑90 (MQ=255)
ccacAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGccc < 2:714777/90‑1 (MQ=255)
ccacAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGccc > 2:488727/1‑90 (MQ=255)
cacaGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGccc < 1:474711/89‑1 (MQ=255)
cacaGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGccc > 2:474711/1‑89 (MQ=255)
caGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAgg < 2:526355/90‑1 (MQ=255)
gTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc < 2:95442/90‑1 (MQ=255)
gTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc < 2:526861/90‑1 (MQ=255)
gTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc < 1:910064/90‑1 (MQ=255)
gTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc > 1:243924/1‑90 (MQ=255)
cacacCCGTTTCCCACCGGGGCCGGATGGCTATCTGCATATTGGCCAGGCGAAATCTATCGGCCTGAACTTCGGGATCGCCCAGGACtat > 2:192521/1‑90 (MQ=255)
cacCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATaa > 1:295405/1‑90 (MQ=255)
gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc < 2:275178/80‑1 (MQ=255)
gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc > 1:275178/1‑80 (MQ=255)
gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGcc > 2:28765/1‑90 (MQ=255)
gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGcc > 1:82853/1‑90 (MQ=255)
gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGcc > 1:508312/1‑90 (MQ=255)
gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGcc > 1:338563/1‑90 (MQ=255)
|
GAAGCCCGCCCGACTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCGCCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCC > NZ_CP009273/701561‑701729
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 29 ≤ 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
CTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCGCCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCCAGTGCAACCTGCGTTTC > NZ_CP009273/701574‑701746
|
CTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACCCCACAGTACACCCCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATAT < SRR3722072.82077/100‑1 (MQ=60)
AACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTG > SRR3722072.866814/1‑100 (MQ=60)
ACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGG < SRR3722072.49030/100‑1 (MQ=60)
ACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGG < SRR3722072.661916/100‑1 (MQ=60)
CTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGC > SRR3722072.189687/1‑100 (MQ=60)
CTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGC < SRR3722072.402222/100‑1 (MQ=60)
CCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCG > SRR3722072.716940/1‑100 (MQ=60)
CATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATC < SRR3722072.667746/100‑1 (MQ=60)
ATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCT > SRR3722072.467082/1‑100 (MQ=60)
GATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGctgtctcttatacacatctccgagcccacgagacgtccgattatct > SRR3722072.66399/1‑54 (MQ=60)
GTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGC > SRR3722072.383081/1‑100 (MQ=60)
GCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAC > SRR3722072.248017/1‑100 (MQ=60)
CCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAA > SRR3722072.300516/1‑100 (MQ=60)
CCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAA < SRR3722072.483363/100‑1 (MQ=60)
GTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCC < SRR3722072.925713/100‑1 (MQ=60)
GTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCC > SRR3722072.84406/1‑100 (MQ=60)
GTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCC > SRR3722072.517466/1‑100 (MQ=60)
GTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCC > SRR3722072.344515/1‑100 (MQ=60)
GTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCC > SRR3722072.279879/1‑100 (MQ=60)
ACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCCAGTGCAACCTGCGTTTC < SRR3722072.219271/100‑1 (MQ=60)
|
CTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCGCCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCCAGTGCAACCTGCGTTTC > NZ_CP009273/701574‑701746
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
