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
A13 F69 I0 R1 1426 148.0 5875178 97.4% 5722423 123.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
JC JC NC_000913 1,293,006 IS1 (+) Δ9 bp 87.2% intergenic (‑84/‑513) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 291401NA (NA)8 (0.060) 6/226 NT 55.3% noncoding (1/768 nt) IS1 repeat region
?NC_000913 = 1293005 7 (0.050)intergenic (‑83/‑522) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
* ? NC_000913 1293015 =7 (0.050)87 (0.630) 62/226 NT 93.1% intergenic (‑93/‑512) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
?NC_000913 = 4519239 NA (NA)noncoding (768/768 nt) IS1 repeat region

CCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/291299‑291401
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAATTCTGAACAACATCCGTACTCTTC  <  NC_000913/1293005‑1292880
                                                                                                                                                                                                                                     
CCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATTCCTGGCTATTGCACAACTGAATTTAAGG                                                                                                <  1:285147/135‑1
CCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATTCCTGGCTATTGCACAACTGAATTTAAGG                                                                                                <  1:512880/135‑1
CCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATTCCTGGCTATTGCACAACTGAATTTAAGG                                                                                                >  2:285147/1‑135
CCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATTCCTGGCTATTGCACAACTGAATTTAAGG                                                                                                >  2:512880/1‑135
                                   AAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAG                                                            >  3:990760/1‑136
                                   AAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAG                                                            <  4:990760/136‑1
                                                        CTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCA                                                                        <  3:939233/103‑1
                                                        CTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCA                                                                        >  4:939233/1‑103
                                                                                                  TCACCCATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAATTCTGAACAACATCCGTACTCTTC  >  3:975849/1‑131
                                                                                                  TCACCCATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAATTCTGAACAACATCCGTACTCTTC  <  4:975849/131‑1
                                                                                                                                                                                                                                     
CCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/291299‑291401
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAATTCTGAACAACATCCGTACTCTTC  <  NC_000913/1293005‑1292880

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A