Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 790,778 G→A 100% intergenic (+277/‑197) kipA_1 → / → ltaS KipI antagonist/Lipoteichoic acid synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE790,7780GA100.0% 117.1 / NA 33intergenic (+277/‑197)kipA_1/ltaSKipI antagonist/Lipoteichoic acid synthase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (15/18);  total (15/18)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTACTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAAT  >  USA300TCH1516_ALE/790641‑790909
                                                                                                                                         |                                                                                                                                   
ttACTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAg                                                                                                                                  <  1:46128/141‑1 (MQ=255)
      gAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCaaa                                                                                                                            >  1:211022/1‑141 (MQ=255)
           ttGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACt                                                                                                                       >  2:56197/1‑141 (MQ=255)
             gACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTg                                                                                                                     >  1:123191/1‑141 (MQ=255)
                     ttACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCa                                                                                                             <  2:353857/141‑1 (MQ=255)
                            atatTTATTAATTGAGCTATGGTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGa                                                                                                      <  2:152027/141‑1 (MQ=255)
                             tatttattAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGaa                                                                                                     >  1:61893/1‑141 (MQ=255)
                                ttattaATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGc                                                                                                  <  1:277463/141‑1 (MQ=255)
                                ttattaATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGc                                                                                                  <  1:294881/141‑1 (MQ=255)
                                 tattaATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCt                                                                                                 <  1:234083/141‑1 (MQ=255)
                                               tGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGACTGATAATATTAAATATAGAAACTTACACAAGCAAATATGAGTTATAGCCCAACATATTTGTTAAATCAACGTCGAAAGCTACAAATAACGataa                                                                                   >  2:5625/1‑141 (MQ=255)
                                                gCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAAt                                                                                  >  2:49710/1‑141 (MQ=255)
                                                          aCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTg                                                                        <  2:211022/141‑1 (MQ=255)
                                                             aTTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAAt                                                                     >  1:193522/1‑141 (MQ=255)
                                                             aTTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTCAAAGCTACAAATAACGAAAATTATAAACTTGAAt                                                                     >  1:349188/1‑141 (MQ=255)
                                                               ttGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCt                                                                   >  1:40375/1‑141 (MQ=255)
                                                                  aTTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGaa                                                                <  2:149163/141‑1 (MQ=255)
                                                                   ttACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGaaa                                                               >  2:320655/1‑141 (MQ=255)
                                                                        aaTTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAAt                                                          <  2:317599/141‑1 (MQ=255)
                                                                            ttAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACt                                                      >  1:44004/1‑141 (MQ=255)
                                                                             tAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATGGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACta                                                     <  2:200002/141‑1 (MQ=255)
                                                                             tAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAGAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACta                                                     <  2:54063/141‑1 (MQ=255)
                                                                                       aaTTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGAc                                           >  1:88450/1‑141 (MQ=255)
                                                                                            aaTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGt                                      <  1:306375/141‑1 (MQ=255)
                                                                                                  aataTTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACtt                                <  1:114253/141‑1 (MQ=255)
                                                                                                    tatTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACtttt                              >  1:338545/1‑141 (MQ=255)
                                                                                                     atTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTa                             <  2:123191/141‑1 (MQ=255)
                                                                                                     atTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTa                             <  1:247583/141‑1 (MQ=255)
                                                                                                                  aCTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACttatta                <  1:115123/141‑1 (MQ=255)
                                                                                                                   cTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTattaa               >  2:352772/1‑141 (MQ=255)
                                                                                                                       cacaAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTAttaattaa           >  1:291307/1‑141 (MQ=255)
                                                                                                                           aGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTAc       <  2:80349/141‑1 (MQ=255)
                                                                                                                                atatGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAAt  <  1:49710/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                   
TTACTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAAT  >  USA300TCH1516_ALE/790641‑790909

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑