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
A9 F59 I0 R1 37 24.7 1037378 89.7% 930528 142.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
JC JC NC_000913 568,268 IS1 (–) +9 bp 92.7% intergenic (+21/‑39) renD → / → emrE DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 19796 =NA (NA)19 (0.720) 18/262 NT 89.8% noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 568276 2 (0.080)intergenic (+29/‑39) renD/emrE DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE
* ? NC_000913 = 258675NA (NA)32 (1.210) 30/264 NT 93.7% noncoding (1/768 nt) IS1 repeat region
?NC_000913 568268 = 2 (0.080)intergenic (+21/‑47) renD/emrE DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE

AGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/19938‑19796
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTTATATACCCTCAATACCCGTTTCATCGCGGCACTCTGGCGACACTCCTTAAAAATCAGATTCGTGCTCACCTTTCCTTCCCATTCTT  <  NC_000913/568276‑568135
                                                                                                                                                                                                                                                                                             
AGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTCTCAATAAGTTGGAGTCATTACC                                                                                                                                                >  2:92135/1‑143
        gacgTGAATCTGAGGCAGCGCCTGGCACGGCTGGGACGGACGTCGCTGTCGTTCTCAAACTCGGTGGAGCTGCATGACAAAGTTATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTT                                                                                                                                        <  2:278213/139‑1
         ACCTGAAGCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTG                                                                                                                                       <  2:128901/143‑1
                 CTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTGCCGTTTGCACTCAAC                                                                                                                               >  1:300051/1‑143
                 CTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAGCTCAAC                                                                                                                               >  1:473468/1‑143
                            CCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATAGGGCATTATCTGAACATAAAACACGATCAATCAGTTGGAGTCGTTCGCTACAGTGCGCACCCAACTCACCTGTTTC                                                                                                                    >  2:469374/1‑143
                             CTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCg                                                                                                                   >  1:166214/1‑142
                               GGCACGGCCGGGACGGAAGTCGCTGTCGTTCTCAAACTCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAACCACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATC                                                                                                                 <  1:3295/143‑1
                                  ACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCATT                                                                                                              >  1:459925/1‑143
                                              GAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTG                                                                                                  >  1:120941/1‑143
                                                        TCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTT                                                                                        <  1:497885/143‑1
                                                             cgCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTTATATA                                                                                   <  2:421831/141‑1
                                                             CTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACGTGTTTCATCATTGTGTTCCCATTGATGTTATTTTATATA                                                                                   >  1:59388/1‑143
                                                                    TCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGACCTAACAACTCCTTTGTCATCTTTGTGTTCCCATTAATCTTCTTTTATATACCCTCAA                                                                            <  1:120025/143‑1
                                                                          GAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTAACAACTGTTTGAACTCAACTCCCCTGTTTCATCATTGTGTTCCCATTGATGTTCTTCTATCTACCCTCAGTACCCG                                                                      >  2:128876/1‑143
                                                                                               GGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGCTCCCATTGATGTTCTTTTATATCCCCCCAATACCCGTTTCATCACGTCCCTCTCGCG                                                 >  2:516376/1‑143
                                                                                                                     ACTATCAATTATTTGTATTTATTACCGATAGTTTGATCTTAACTCACCTGGTTCATCATTGTGTTCCCATTTATGTTCTTTTATATACCCTCAATACCCGTTTCATCGCGGCACTCTGGCGACACTCCTTAAAAATCAGATTC                           <  2:351881/143‑1
                                                                                                                         TCAATAAGTTGGAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTTATATACCCTCAATACCCGTTTCATCGCGCCACTCTGCCCACACCCCTTAACAATCCAACTCGTGC                       >  1:502181/1‑143
                                                                                                                                    GAGTCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTTATATACCCTCAATACCCGTTTCATCGCGGCACTCTGGCGACCCTCCTTAAAAATCAGATTCGTGCTCACCTTTCCT            >  1:344676/1‑143
                                                                                                                                       TCATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTTATATACCCTCAATACCCGTTTCATCGCGGCACTCTGGCGACACTCCTTAAAAATCAGATTCGTGCTCACCTTTCCTTCC         <  1:30530/143‑1
                                                                                                                                         ATTACCTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTTATATACCCTCAATACCCGTTTCATCGCGGCACTCTGGCGACACTCCTTAAAAATCAGATTCGTGCTCACCTTTCCTTCCCA       <  1:489256/143‑1
                                                                                                                                              CTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTTATATACCCTCAATACCCGTTTCATGGAGGCACTCTGGCGACACTCCTTAAAAATCAGATTCGTGCTCACCTTTCCTTCCCCTTCTT  >  2:309911/1‑143
                                                                                                                                                                                                                                                                                             
AGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/19938‑19796
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cTACAGTTTGAACTCAACTCACCTGTTTCATCATTGTGTTCCCATTGATGTTCTTTTATATACCCTCAATACCCGTTTCATCGCGGCACTCTGGCGACACTCCTTAAAAATCAGATTCGTGCTCACCTTTCCTTCCCATTCTT  <  NC_000913/568276‑568135

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ 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