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% 214.6 / NA 64L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (28/36);  total (28/36)

ATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAA  >  USA300TCH1516_ALE/1513794‑1514066
                                                                                                                                        |                                                                                                                                        
atttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTAttt                                                                                                                                      >  2:87292/1‑140 (MQ=255)
   tatttGTATTTATCGCTTTATTAGTAGACATTGGAATGGGGTTGGTCTCTTGGAAAAAAAATAAAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAt                                                                                                                                   <  2:570207/141‑1 (MQ=255)
   tagttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAt                                                                                                                                   <  2:1063595/138‑1 (MQ=255)
    atttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAtt                                                                                                                                  <  2:368611/141‑1 (MQ=255)
    atttGTATGTATCGCTTGATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAtt                                                                                                                                  <  2:209793/141‑1 (MQ=255)
        gtatgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGa                                                                                                                              >  1:755898/1‑141 (MQ=255)
        gtatgtatCGCTTTATTAGTAGCCATTGGCATGGGGTATGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGa                                                                                                                              >  1:486058/1‑141 (MQ=255)
           tgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatta                                                                                                                           <  1:469755/141‑1 (MQ=255)
           tgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatta                                                                                                                           <  1:505753/141‑1 (MQ=255)
             tatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGattatt                                                                                                                         >  1:851679/1‑141 (MQ=255)
             tatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGattatt                                                                                                                         >  2:686866/1‑141 (MQ=255)
                      attaGTAGCACTTGGCATGGAGTTTGTATCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACAGCGCGTAAAAAACCCATCATCTATATCACTCATAATATCTGCTTTTGGAGTAGGATTATTAATGCCatt                                                                                                                <  2:256282/141‑1 (MQ=255)
                        tagtagCCATTGGCATGGGGTTGGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                                              <  1:1074884/141‑1 (MQ=255)
                            agCCATTTGCAATGGGTTTGACTCATGGATAAAGCATACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                                          <  2:1015563/141‑1 (MQ=255)
                                 ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCTATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                     >  2:761091/1‑141 (MQ=255)
                                 ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCGATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                     >  2:1174600/1‑141 (MQ=255)
                                 ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCGATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATATTTTGGATTAt                                                                                                     >  2:767973/1‑141 (MQ=255)
                                  tGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATc                                                                                                    <  1:604097/141‑1 (MQ=255)
                                    gCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                                  >  1:197417/1‑141 (MQ=255)
                                     cATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACt                                                                                                 <  2:1036375/141‑1 (MQ=255)
                                      aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                                >  1:799088/1‑141 (MQ=255)
                                      aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                                >  1:780875/1‑141 (MQ=255)
                                      aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                                >  1:928725/1‑141 (MQ=255)
                                      aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                                <  2:1160125/141‑1 (MQ=255)
                                        ggggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTAt                                                                                              <  1:939204/141‑1 (MQ=255)
                                        ggggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTAt                                                                                              >  2:810828/1‑141 (MQ=255)
                                           gTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCt                                                                                           <  2:845015/141‑1 (MQ=255)
                                            tttGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAGTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCtt                                                                                          >  2:111372/1‑141 (MQ=255)
                                              tGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGt                                                                                        >  2:95228/1‑141 (MQ=255)
                                                     tGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTtata                                                                                 <  1:930888/141‑1 (MQ=255)
                                                       gATAAAGCGTACAACAAATACGGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATCTTTTATTGTATTGGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAt                                                                               >  2:818106/1‑141 (MQ=255)
                                                       gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTTATGCCATTATTTAAATTCTCACTTCTCCTTGAATTtatact                                                                               <  2:1182074/141‑3 (MQ=255)
                                                         tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTg                                                                             <  2:1054850/141‑1 (MQ=255)
                                                         aaaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTg                                                                             <  2:1189156/140‑1 (MQ=255)
                                                          aaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTTTTTATAATTGa                                                                            >  2:674470/1‑141 (MQ=255)
                                                             gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTGTGTCTTATCCGCGTATTTATATTGGAAtt                                                                         >  1:562161/1‑141 (MQ=255)
                                                               gTACAAAAAATACTGCAATAAATGTACCACATCGAGTAAAAAAACAAGCCACTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCATTTTTTTGGATTATCACTTATACTTGTTTTTATGATGGAATTaa                                                                       >  2:126657/1‑141 (MQ=255)
                                                                aaCAAAAAAGACTGCAATAAAAGTACCACATCGCGTAAAAAAACCCGCATCTATATCCCTTATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAat                                                                      <  2:94270/140‑1 (MQ=255)
                                                                      aaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtata                                                                >  1:1172840/1‑141 (MQ=255)
                                                                        aTACTGCAATACAAGTACCACATCGCGTAAACAAACCAGCATCTCTATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtatata                                                              <  1:576884/141‑1 (MQ=255)
                                                                        aTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTGATATtatatt                                                              >  2:1190927/1‑140 (MQ=255)
                                                                        aTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtataga                                                              >  2:1192429/1‑139 (MQ=255)
                                                                           cTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                           <  1:638716/141‑1 (MQ=255)
                                                                                  aaaaGTACCACATTGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTCTAATTGAAGCCATATTATATATTAAAGAtcg                                                    <  1:287522/141‑1 (MQ=255)
                                                                                   aaaTTACCACATCGCTTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgt                                                   <  2:221545/141‑1 (MQ=255)
                                                                                   aaaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgt                                                   <  2:74771/141‑1 (MQ=255)
                                                                                    aaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAGTGAATTAATATTATATATTAAAGAtcgtc                                                  <  2:10593/141‑1 (MQ=255)
                                                                                      atACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATcgtcgt                                                <  2:1119687/140‑1 (MQ=255)
                                                                                          cacaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTa                                            >  1:1179318/1‑141 (MQ=255)
                                                                                          cacaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTa                                            >  2:1161197/1‑141 (MQ=255)
                                                                                          cacaCCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTa                                            <  1:950918/141‑1 (MQ=255)
                                                                                               cccgTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGCTCACCACTCCTCCTTATATTTATCAGTGAACGAATATTGTAGATTAAAGATCGTGGTGCTAAACaa                                       <  2:1128416/139‑1 (MQ=255)
                                                                                                gcgTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaat                                      <  1:1094203/141‑1 (MQ=255)
                                                                                                ccgTAAAAAAACCAGCATCTATATCACTCATAATATTTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaat                                      <  1:1028563/140‑1 (MQ=255)
                                                                                                           ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa                           <  2:799088/141‑1 (MQ=255)
                                                                                                           ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa                           <  2:928725/141‑1 (MQ=255)
                                                                                                                      atCACTCATTATATTTTTTATTGTACTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACt                <  2:533178/141‑1 (MQ=255)
                                                                                                                         aCTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGAc             <  1:810828/141‑1 (MQ=255)
                                                                                                                              taataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCTTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACATTAATGCACTTAAAGTTTTGTACTGACGAAAt        >  1:816036/1‑141 (MQ=255)
                                                                                                                               aataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAtt       >  1:1068771/1‑141 (MQ=255)
                                                                                                                                ttatGTTTTGTTGTATTAGGATTATTAATGTTGTCTTTTGGATGATCACTTATCCTTGTATTTATAATTGAATTAATATTATAGATTAAAGCTCGTCGTGCTAAACAATGAGGCACTTCAAGTTTTGAACTGACGAAAttt      <  2:204442/140‑1 (MQ=255)
                                                                                                                                 tatGTTTTATTGTATTAGGATTATTAATGCCATTGTTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTa     <  1:942086/141‑1 (MQ=255)
                                                                                                                                    gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTCAAGTTTTGAACTGACGAAATTTACaa  >  1:12434/1‑141 (MQ=255)
                                                                                                                                    gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTATATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATACACTTAAAGTTTTGAACTGACGAAATTTACaa  >  2:347688/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                        
ATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAA  >  USA300TCH1516_ALE/1513794‑1514066

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑