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
A19 F106 I1 R1 27 57.4 1363720 95.8% 1306443 135.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 1,513,930 A→T L413F (TTA→TTT)  USA300HOU_RS07375 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,513,9300AT100.0% 68.5 / NA 23L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (13/10);  total (13/10)

ATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATT  >  USA300TCH1516_ALE/1513808‑1514061
                                                                                                                          |                                                                                                                                   
atCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAATAAACCAGCATCTATATCACTCTTAATATGTTTTATTGTATTAGGa                                                                                                                         <  1:511797/135‑1 (MQ=255)
        attaATAACCATGGGCATGGGGCTTGCCCCCTAGATAAAGCGTACAAAAAATACCGCAATAAAAGTACCACATCGAGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAAt                                                                                                                 <  2:348581/135‑1 (MQ=255)
           agcagCCAGTGGCATGGGTCTTGTCTCTTGGACAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCTTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                              <  1:135116/132‑1 (MQ=255)
            gtagCCATTGCCATCGGGATTGTCTCTTGGATAAAGCATACAAGAAATACTGCAATCAACGTGCCACATAGCGTAAAACAACCAGTATCTATATCACTCATAATATGTTTTATTGTATTAGGATTCTTAATGCCa                                                                                                             >  1:472982/1‑135 (MQ=255)
             tagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                            >  1:476801/1‑135 (MQ=255)
             tagCCATTGGCATGGGGATTGTCTCTTGGATAAAGCGTACAAAAAATAATGCAATAAAAGTACAACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                            >  1:616328/1‑135 (MQ=255)
                         tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACCTTGCTTTAAAAAACCAGCATCTTTATCACTTTTAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                <  1:266970/135‑1 (MQ=255)
                         tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                <  2:325732/135‑1 (MQ=255)
                           gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                              >  1:576437/1‑135 (MQ=255)
                            ggTTTGTCTCTTGGATAAAGCGTACAAAAAATACAGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                             >  1:60991/1‑135 (MQ=255)
                                tGTCTCTTGGATAAAGCGTACAAAAAATACTACAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTAt                                                                                         >  1:474085/1‑135 (MQ=255)
                                     ctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTTTTTGTATTATCACTTATCCTTg                                                                                    <  1:477441/135‑1 (MQ=255)
                                            aaaGTGCACAAAAAATACTGGAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTtat                                                                             <  2:273867/135‑1 (MQ=255)
                                            aaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAAACAGTTATTCTATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTTTTTGGATTATCACTTATCCTTGTATTtat                                                                             <  1:659590/135‑1 (MQ=255)
                                              aGCGTACAAAAAACACTGCAATAAAAGTACCACATCGCGTAAAAAATCCGGCTTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATaa                                                                           <  1:615201/135‑1 (MQ=255)
                                                                                      aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACa                                   >  1:501575/1‑135 (MQ=255)
                                                                                      aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACa                                   >  1:60269/1‑135 (MQ=255)
                                                                                      aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACa                                   >  1:316295/1‑135 (MQ=255)
                                                                                      aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACa                                   >  1:268818/1‑135 (MQ=255)
                                                                                              cAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATCTTAAAGATCGTCGTGTTAAACAATAATGCa                           >  2:608464/1‑135 (MQ=255)
                                                                                              cAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTACTGCTAAACAATAATGCa                           >  2:617365/1‑135 (MQ=255)
                                                                                                    cTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaaa                     >  1:593346/1‑135 (MQ=255)
                                                                                                          cACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTACAGTTTTg               <  2:60991/135‑1 (MQ=255)
                                                                                                                       ttttATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAtt  >  1:47642/1‑135 (MQ=255)
                                                                                                                       ttttATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAtt  >  2:89725/1‑135 (MQ=255)
                                                                                                                          |                                                                                                                                   
ATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATT  >  USA300TCH1516_ALE/1513808‑1514061

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A