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% 213.3 / NA 65L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (29/36);  total (29/36)

ATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  USA300TCH1516_ALE/1513794‑1514065
                                                                                                                                        |                                                                                                                                       
atttatttGTATGTATGGATTTAGTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCAAAAAAAAAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTAtt                                                                                                                                      <  2:521541/140‑1 (MQ=255)
 tttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGAGTACAAAAAATACTCCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTg                                                                                                                                     <  2:224852/140‑1 (MQ=255)
    ttttGTATTTATCGTTTTTTTAGTAGCCAGTGGCATGGGGTTTGTCTCTTGTATAAAGCGTACAAAAAATACTGCTATAAAAGTAAAAAAAAAAATAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAt                                                                                                                                  <  2:451829/139‑1 (MQ=255)
     tttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTCtt                                                                                                                                 >  2:55062/1‑140 (MQ=255)
       tgtatgtaTCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAg                                                                                                                               >  1:404272/1‑140 (MQ=255)
        gtatgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAgg                                                                                                                              >  1:518984/1‑140 (MQ=255)
                cGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTaa                                                                                                                      >  2:844234/1‑140 (MQ=255)
                  cTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                                    <  1:57554/140‑1 (MQ=255)
                      attaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                                >  1:797568/1‑140 (MQ=255)
                      attaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                                >  1:748255/1‑140 (MQ=255)
                      attaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                                >  1:315015/1‑140 (MQ=255)
                       ttaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatt                                                                                                               >  1:379395/1‑140 (MQ=255)
                         agtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCACCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATACCattat                                                                                                             >  1:335499/1‑140 (MQ=255)
                          gtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattatt                                                                                                            <  2:730154/140‑1 (MQ=255)
                           tagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATCTGTTTTATTGTATTAGGATTATTAATGCCATTAttt                                                                                                           >  1:620567/1‑140 (MQ=255)
                            agCCATTGGTATGGGGTTTTGCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                          <  2:856420/140‑1 (MQ=255)
                                  tGGCTTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                    <  1:966849/140‑1 (MQ=255)
                                  ctgCATGGGGTTTATGTATTGGAAAAACCGTAAAAAAAATACTGCAATAAAAGTACCCCATAGCGTAAAAAAACCAGCCTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                    <  2:453567/138‑1 (MQ=255)
                                  agggaTGGGGTTTGTCTCTTGGAGAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCAATCATTATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                    <  1:282158/136‑1 (MQ=255)
                                   ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATc                                                                                                   >  1:21071/1‑140 (MQ=255)
                                    gcagtgggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTTGGGTGACAATTGTCATTATTTGGATTATCa                                                                                                  <  1:486607/135‑1 (MQ=255)
                                        ggggTTTGTTTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                              <  1:255484/140‑1 (MQ=255)
                                        ggggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTTATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                              <  1:909202/140‑1 (MQ=255)
                                          ggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATc                                                                                            <  2:881998/140‑1 (MQ=255)
                                            ttggTCTCTTGGATAAAACGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGATTTATTGTATTAGGATGATTAATGCCAGTCTTTGGATTATCACTAATCCt                                                                                          >  2:148622/4‑140 (MQ=255)
                                               gtttgttGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCCTGt                                                                                       <  2:93786/135‑1 (MQ=255)
                                                tctcTTGAGTAAAGCGGACAAAAAAGACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                      <  2:615033/140‑1 (MQ=255)
                                                gctctTGAATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                      <  2:513240/139‑1 (MQ=255)
                                                 ctctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAt                                                                                     <  2:518412/140‑1 (MQ=255)
                                                 ctctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATAACTCATCTTTCTac                                                                                     >  2:902059/1‑139 (MQ=255)
                                                    ttGGATAAATCGTACAAAAAATACTGCAATAAAAGTACCACATCGTGTAAAAAAACCAGCATCTATATCCCTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTta                                                                                  <  2:867104/140‑1 (MQ=255)
                                                      ggATAAATCCTAAAAAAAATACTGCAAGAAAAGTACCACATCGCGTAAAAAGACCCGCATCTATATCACTCATAATATGTTTTATCGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTtata                                                                                <  1:282045/140‑1 (MQ=255)
                                                      ggATAAAGCGTACAAAAAATACCGCAATAAAAGCACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTtata                                                                                <  1:765321/140‑1 (MQ=255)
                                                        aTAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAt                                                                              <  1:999427/140‑1 (MQ=255)
                                                          tgaGCGAACAAAACATACGGCAATAAAAGATACACATCGTGTAAAAATCCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTCTTTTGATTATCACTTATCCTTGTATTTATAATTg                                                                            <  2:730242/138‑1 (MQ=255)
                                                          aaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCTTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTg                                                                            <  2:51749/140‑1 (MQ=255)
                                                            aGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                          >  2:25213/1‑140 (MQ=255)
                                                            aGCGAACATAAAAAACTGCAATAAAAGTACCCCAGCGCGTACAAAAGCCGGCATCTATATCACTCATAATATGTTATATTGTACTAGGATTATTATTGCCATTATGTTGATTATCAATTATCCTGTTATTTATAATTGaa                                                                          >  2:212080/1‑140 (MQ=255)
                                                             gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                         <  2:323396/140‑1 (MQ=255)
                                                              cGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                        <  1:946310/140‑1 (MQ=255)
                                                                tACAAAAAATACTGCAATACAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTAGGATTATCCCTTATCCTTGTATTTATAATTGAATTaa                                                                      >  1:653241/1‑140 (MQ=255)
                                                                tACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTaa                                                                      >  1:138946/1‑140 (MQ=255)
                                                                    aaaaaTACTGCAATAAAAGTACCACATCGCGT‑AAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTATTTTAATGTTGAGTTGTATCACTTATCATTGTATTTATAATTGAATTAatataa                                                                 >  1:572611/1‑138 (MQ=255)
                                                                     aaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                                 <  1:104278/140‑1 (MQ=255)
                                                                     aaaaTAATGCGATGAAAGTACCACCTCGCGTAAAAAAACCAGCATCTATATCCCTCATCATATGTTTTATTGTAGTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                                 <  1:66267/140‑1 (MQ=255)
                                                                        aTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTCTTTGCCACATCGCTTATCCTTGTATTTATAATTGAATTAATATtatat                                                              >  1:937088/1‑140 (MQ=255)
                                                                        aTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTAAATTAATATtatat                                                              >  1:161236/1‑140 (MQ=255)
                                                                            tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                          >  2:809973/1‑140 (MQ=255)
                                                                                aTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCCCTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGa                                                      <  1:566817/140‑1 (MQ=255)
                                                                                     atgaCCACATCGCTTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtc                                                 <  2:959185/137‑1 (MQ=255)
                                                                                     aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtc                                                 <  1:310036/140‑1 (MQ=255)
                                                                                     aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAAGATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTAAATTAATATTATATATTAAAGAtcgtc                                                 >  1:567674/1‑140 (MQ=255)
                                                                                         ccACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                                             >  1:145078/1‑140 (MQ=255)
                                                                                             aTCGCTTAAAAAAACCAGCCTCTCTCTCACTCATAATATGTTTTGTTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATTTTAAAGATCGTCGTGCTaaa                                         <  1:706053/140‑1 (MQ=255)
                                                                                             aTCGCGTAAAACAACCAGCATCTATATCACTCATAATATGTTTTATTTTATTAGGGTTATTAATGCCATTATTAGGATTATCACTTATCCTTGTATTTAGAATTGAATAGATATTACATATGAAGGATCGTCGTACTaaa                                         <  1:740670/140‑1 (MQ=255)
                                                                                                       aaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATCTTATATATTAAAGATCGTCGGGCTAAAAAATAATGCa                               >  1:449144/1‑140 (MQ=255)
                                                                                                       aaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCa                               <  2:767637/140‑1 (MQ=255)
                                                                                                         aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                             <  2:379395/140‑1 (MQ=255)
                                                                                                          aCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACtt                            <  1:117170/140‑1 (MQ=255)
                                                                                                           ccAGCCTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTACTGCCATTATTTGGATTATCCTTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGACCTTa                           >  1:397714/1‑140 (MQ=255)
                                                                                                                          cTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTATACAATAATGCACTTAAAGTTTTGAACTGAc            >  1:160359/1‑140 (MQ=255)
                                                                                                                              taataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGaaa        <  1:442888/140‑1 (MQ=255)
                                                                                                                               aataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATAGAATTAATATTATATACGAAATTTCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAt       >  1:189367/1‑140 (MQ=255)
                                                                                                                                  atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTa    >  1:158979/1‑140 (MQ=255)
                                                                                                                                    gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAATTTTGAACTGACGAAATTTACa  >  1:63002/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                       
ATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  USA300TCH1516_ALE/1513794‑1514065

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: ‑