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
A0 F0 I1 R1 87 31.3 1776092 98.2% 1744122 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,887,571 Δ1 bp intergenic (+163/+7) sokX → / ← cysH small RNA SokX/phosphoadenosine phosphosulfate reductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,887,5700G.100.0% 89.4 / NA 20intergenic (+162/+8)sokX/cysHsmall RNA SokX/phosphoadenosine phosphosulfate reductase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (13/7);  total (13/7)

ACGTTTAAAATCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCCGGCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTTTCTTCTTCCGCCATGCCG  >  NC_000913/2887495‑2887644
                                                                           |                                                                          
aCGTTTAAAATCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAata                                                                      >  1:519588/1‑81 (MQ=255)
 cGTTTAAAATCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAatat                                                                     >  2:519584/1‑81 (MQ=255)
      aaaaTCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTAcc                                                                >  1:519592/1‑81 (MQ=255)
         aTCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCtt                                                             >  2:519590/1‑81 (MQ=255)
           cAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCg                                                           >  2:519583/1‑81 (MQ=255)
              gAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCgtg                                                         >  1:519587/1‑80 (MQ=255)
                  gctgctCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAAcc                                                    >  2:519589/1‑81 (MQ=255)
                   ctgctCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAAccc                                                   <  1:519566/81‑1 (MQ=255)
                   ctgctCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAAccc                                                   <  2:519565/81‑1 (MQ=255)
                   ctgctCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAAccc                                                   <  1:519567/81‑1 (MQ=255)
                   ctgctCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAAccc                                                   <  1:519564/81‑1 (MQ=255)
                         gCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTc                                             >  2:519586/1‑81 (MQ=255)
                               tAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCtttt                                       <  1:519568/81‑1 (MQ=255)
                                   aaCGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAg                                   >  1:519585/1‑81 (MQ=255)
                                              catTTCTGACAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAAcg                        >  2:519599/1‑81 (MQ=255)
                                                      aCAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTttctt                >  1:519594/1‑81 (MQ=255)
                                                      aCAGAGGCGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTttct                 <  1:519569/80‑1 (MQ=255)
                                                             cGTTTAATTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTTTCTTCTTCCGc         >  2:519595/1‑81 (MQ=255)
                                                                   aTTTGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTTTCTTCTTCCGCCATGcc   <  2:519570/81‑1 (MQ=255)
                                                                    tttGTCC‑GCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTTTCTTCTTCCGCCATGCCg  >  2:519605/1‑81 (MQ=255)
                                                                           |                                                                          
ACGTTTAAAATCAGGAATGCTGCTCGCAAAATAAAAACGCCCCCATCATTTCTGACAGAGGCGTTTAATTTGTCCGGCAATATTTACCCTTCGTGTAACCCACATTCCCTTTTTAAGCCAAAGAAACGCGTTTCTTCTTCCGCCATGCCG  >  NC_000913/2887495‑2887644

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A