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% 177.1 / NA 56intergenic (+277/‑197)kipA_1/ltaSKipI antagonist/Lipoteichoic acid synthase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/28);  total (28/28)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTAAT  >  USA300TCH1516_ALE/790644‑790915
                                                                                                                                      |                                                                                                                                         
cTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGccc                                                                                                                                     >  2:661695/1‑141 (MQ=255)
   gAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCaaa                                                                                                                                  >  1:223436/1‑141 (MQ=255)
   gAAGTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCaaa                                                                                                                                  <  1:250057/141‑1 (MQ=255)
      ttttGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATa                                                                                                                               <  1:209033/141‑1 (MQ=255)
       tttGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATAc                                                                                                                              <  1:525328/141‑1 (MQ=255)
             tAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGATa                                                                                                                        >  2:132442/1‑141 (MQ=255)
                  ttACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCa                                                                                                                   <  1:111862/141‑1 (MQ=255)
                       ctATATTTATTAATTGAGCTATGCTTAGTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAGGAAACTTACCCCCGCAGAGAGGATTGATAGCCCAAAATACTTGTTAAATCAAAGtt                                                                                                              <  1:371441/141‑1 (MQ=255)
                        tataTTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAGATACTTGTTAAATCAAAGTTg                                                                                                             <  1:625141/141‑1 (MQ=255)
                               attaATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAACTCAAAGTTGAAAGCTa                                                                                                      <  1:396092/141‑1 (MQ=255)
                                 taATTGAGCTATGCTTATTATTACAATTTGATTACAACTTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAAAACTTGTTAAATCAAAGTTGAAAGATACa                                                                                                    >  2:140461/1‑141 (MQ=255)
                                 taATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACa                                                                                                    >  1:740680/1‑141 (MQ=255)
                                  aaTTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACaa                                                                                                   >  1:67498/1‑141 (MQ=255)
                                     tGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATa                                                                                                >  1:271594/1‑141 (MQ=255)
                                      gAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATaa                                                                                               <  1:208168/141‑1 (MQ=255)
                                        gCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACg                                                                                             >  1:61936/1‑141 (MQ=255)
                                           aTGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGaaa                                                                                          <  1:216805/141‑1 (MQ=255)
                                             gCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAAAGAAAAt                                                                                        >  1:475385/1‑141 (MQ=255)
                                                    attaCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGTAACTTACTAAAGCAAATACTATGTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAAc                                                                                 <  2:664463/141‑1 (MQ=255)
                                                       aCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACACATAACGAAAATTATACACTTg                                                                              >  1:478170/1‑141 (MQ=255)
                                                        cAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGCAAATTATAAACTTGa                                                                             <  1:386367/141‑1 (MQ=255)
                                                         aaTTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGaa                                                                            >  1:553314/1‑141 (MQ=255)
                                                             tGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTg                                                                        >  1:278642/1‑141 (MQ=255)
                                                             tGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTg                                                                        >  1:692908/1‑141 (MQ=255)
                                                              catcacgaaTTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGa                                                                       >  2:91567/8‑141 (MQ=255)
                                                                  aCAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGaaaaa                                                                   >  2:249169/1‑139 (MQ=255)
                                                                       ttttAAATTCGCTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTa                                                              <  1:119936/141‑1 (MQ=255)
                                                                            aaTTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACtata                                                         >  1:419817/1‑141 (MQ=255)
                                                                             aTTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATaa                                                        >  2:96357/1‑141 (MQ=255)
                                                                             aTTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTCGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATaa                                                        >  1:291316/1‑141 (MQ=255)
                                                                                          aTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGtt                                           <  2:268736/141‑1 (MQ=255)
                                                                                            aataataTTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTaa                                         <  2:443403/140‑1 (MQ=255)
                                                                                             ataataTTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAAc                                        <  1:132442/141‑1 (MQ=255)
                                                                                             ataataTTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAAc                                        >  2:101801/1‑141 (MQ=255)
                                                                                              taataTTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACt                                       <  1:661695/141‑1 (MQ=255)
                                                                                              aaataCTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACt                                       <  2:188917/140‑1 (MQ=255)
                                                                                                 tatTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACtttt                                    <  1:326659/141‑1 (MQ=255)
                                                                                                    taaataaaGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTaaa                                 <  2:23969/141‑1 (MQ=255)
                                                                                                     aaataaaGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGCCAATGTTAACttttcacc                                >  2:380282/1‑137 (MQ=255)
                                                                                                        taaaGAAACTTACACAAGCAAAGATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATCATGACAATGTTAACTTTTAAACGCa                             <  1:389251/141‑1 (MQ=255)
                                                                                                         aaaGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCAc                            <  1:462725/141‑1 (MQ=255)
                                                                                                         aaaGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCAc                            <  2:61936/141‑1 (MQ=255)
                                                                                                           aGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGAc                                                 <  2:270476/118‑1 (MQ=255)
                                                                                                           aGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGAc                                                 >  1:270476/1‑118 (MQ=255)
                                                                                                            gAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACtta                         <  2:223436/141‑1 (MQ=255)
                                                                                                                  tACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTattaatt                   >  1:757571/1‑141 (MQ=255)
                                                                                                                  tACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTattaatt                   >  1:641876/1‑141 (MQ=255)
                                                                                                                     acaAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAAc                <  1:393315/141‑1 (MQ=255)
                                                                                                                       aaGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCAACAAATAACGAAAATTATAAACTTGAAGCTGAAAGTAATTACTATAATTATGACAATGGTAACTTTTAAACGCACTTATTAATTAACTa              <  2:67498/141‑1 (MQ=255)
                                                                                                                        aGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAGCGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGCCAGTGTTAACTTTTAAACGCACTTATTAATGAACTaa             >  1:259180/1‑140 (MQ=255)
                                                                                                                        aGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTAc             <  2:740680/141‑1 (MQ=255)
                                                                                                                        aGCAAATATGAGTTATAGCCCAAAATACATGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTAc             >  1:491581/1‑141 (MQ=255)
                                                                                                                           caattggAGTTATAGCCCAAAATACTTGTTAAATCAAAGTGGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATa          <  1:4769/135‑1 (MQ=255)
                                                                                                                                tGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAACGtt     >  2:190318/1‑141 (MQ=255)
                                                                                                                                tGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACAAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGAACTTATTACTTAGATAAAAAATGtt     >  2:325098/1‑141 (MQ=255)
                                                                                                                                   gTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTAat  >  2:629581/1‑141 (MQ=255)
                                                                                                                                      |                                                                                                                                         
CTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTAAT  >  USA300TCH1516_ALE/790644‑790915

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑