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
A11 F22 I0 R1 49 16.0 500808 99.2% 496801 149.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
JC JC NC_000913 3,966,263 IS1 (+) +9 bp 31.6% intergenic (+173/‑146) trxA → / → rho thioredoxin 1/transcription termination factor

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 3583428 =NA (NA)7 (0.470) 5/278 NT 33.5% noncoding (1/768 nt) IS1 repeat region
?NC_000913 = 3966271 13 (0.940)intergenic (+181/‑146) trxA/rho thioredoxin 1/transcription termination factor
* ? NC_000913 = 3584195NA (NA)5 (0.340) 5/278 NT 26.4% noncoding (768/768 nt) IS1 repeat region
?NC_000913 3966263 = 13 (0.940)intergenic (+173/‑154) trxA/rho thioredoxin 1/transcription termination factor

TAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3583571‑3583428
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GACGGATTGAGTGACGAGCCAGAAATCTGTTCACTTCGCATTTAAGATAAAACGGGAAGCGTTGGAAATTACAAGATTCAAACTTAATAAGGTATGTTTAATACGAAGTCAACACTAAGTTAGCATGACTCACGCCGG  <  NC_000913/3966271‑3966134
                                                                                                                                                                                                                                                                                          
TAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGAACCACCCCGTCAGTAGCTGAACTGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGACGGA                                                                                                                                      <  1:165839/150‑1
               GCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGACGGATTGAGTGACGAGCCA                                                                                                                       <  2:46044/150‑1
               GCGGTGCTTTTGCCGTTACGCACCACCCCCTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGACGGATTGAGTGACGAGCCA                                                                                                                       <  2:166849/150‑1
                                                                          AGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGACGGATTGAGTGACGAGCCAGAAATCTGTTCACTTCGCATTTAAGATAAAACGGGAAGCGTTGGAAATTACAAGATTCA                                                            >  2:248897/1‑150
                                                                                  AAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGACGGATTGAGTGACGAGCCAGAAATCTGTTCACTTCGCATTTAAGATAAAACGGGAAGCGTTGGAAATTACAAGATTCAAACTTAAT                                                    >  2:184233/1‑150
                                                                                  AAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGACGGATTGAGTGACGAGCCAGAAATCTGTTCACTTCGCATTTAAGATAAAACGGGAAGCGTTGGAAATTACAAGATTCAAACTTAAT                                                    >  2:30215/1‑150
                                                                                                                                    GGCAGCATCACCGACGGATTGAGTGACGAGCCAGAAATCTGTTCACTTCGCATTTAAGATAAAACGGGAAGCGTTGGAAATTACAAGATTCAAACTTAATAAGGTATGTTTAATACGAAGTCAACACTAAGTTAGCATGACTCACGCCGG  >  2:43661/1‑150
                                                                                                                                                                                                                                                                                          
TAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3583571‑3583428
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GACGGATTGAGTGACGAGCCAGAAATCTGTTCACTTCGCATTTAAGATAAAACGGGAAGCGTTGGAAATTACAAGATTCAAACTTAATAAGGTATGTTTAATACGAAGTCAACACTAAGTTAGCATGACTCACGCCGG  <  NC_000913/3966271‑3966134

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ 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