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_ALE1,513,9300AT98.4% 193.1 / ‑4.9 61L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base T (36/24);  total (36/25)
Fisher's exact test for biased strand distribution p-value = 4.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

ATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAA  >  USA300TCH1516_ALE/1513794‑1514066
                                                                                                                                        |                                                                                                                                        
atttattgGTATGTATCGCTTTATTAGGAGTCATAGGCATTGGGTTCGTATCGTGAATAAAGCGTACAAAAAATACTGCAATAAAAGTAACACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTg                                                                                                                                      <  2:667454/141‑1 (MQ=255)
      ttGTATGTATCGCTTTATTAGTAGCCATTGGCGTGGGGTTTGTCTCTTGGATAAAGTGCACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAg                                                                                                                                >  1:927786/1‑141 (MQ=255)
      ttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAATGAGAACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAg                                                                                                                                >  1:927776/1‑141 (MQ=255)
           tgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGattt                                                                                                                           >  1:622096/1‑140 (MQ=255)
                 gCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGGTTTATTGTATTAGGATTATTAATg                                                                                                                     >  1:444056/1‑141 (MQ=255)
                 gCTTTATTAGTAGCCATTGGCATGGGGTTCGTCGCTTGGATAAAGCGTACAAAAAAAACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCGTACTATGATTTATTGTTTTAGGATTATTAATg                                                                                                                     >  1:791349/1‑141 (MQ=255)
                       ttaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatta                                                                                                               >  1:906416/1‑141 (MQ=255)
                       taagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatta                                                                                                               >  2:117864/3‑141 (MQ=255)
                        tagtagACATTGGCAAGGGGTTTGCCTTTTGAATAAACCATACAAAAAATACTGCAATAAAAGTACCATATCGCGTAAAAAAACCAGTATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                                              <  2:750961/141‑1 (MQ=255)
                             gCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGa                                                                                                         <  2:808108/141‑1 (MQ=255)
                             gCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACCCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGa                                                                                                         <  1:56485/141‑1 (MQ=255)
                               cATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATACCATTATTTGGAtt                                                                                                       >  2:152907/1‑141 (MQ=255)
                                 ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                     >  1:777376/1‑141 (MQ=255)
                                   ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGCTTATCa                                                                                                   >  2:931145/1‑141 (MQ=255)
                                   ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                   <  2:877098/141‑1 (MQ=255)
                                    gCATGGGGTGTGGTTGTGGGATAAAGCGTACAAAAAATATTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTTGGATTATTAATGCCATTATTTGGATTATCAc                                                                                                  <  2:613641/141‑1 (MQ=255)
                                      aTGGGGTTTGCCTCTTGGATAATGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATAGGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                                <  1:257586/141‑1 (MQ=255)
                                          ggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATcc                                                                                            <  1:984483/141‑1 (MQ=255)
                                               gTCTCTTGTATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                       <  1:789556/141‑1 (MQ=255)
                                                         tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTg                                                                             >  2:762624/1‑141 (MQ=255)
                                                          aaaGCGAACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                            <  1:164895/141‑1 (MQ=255)
                                                            aGCTTACAAAAAATACTGCAATAAAAGTCGCACATCGCGTAAAAATACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                          <  2:912218/141‑1 (MQ=255)
                                                            aGCGTACAAAAAATACTGCAATAAAAGTACCACCTCGCGTAAAAAAACCCGCACCGATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                          >  1:233017/1‑141 (MQ=255)
                                                            aGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                          >  1:745791/1‑141 (MQ=255)
                                                            aGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                          >  1:427468/1‑141 (MQ=255)
                                                                 aCAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAata                                                                     >  2:121257/1‑141 (MQ=255)
                                                                    aaaaaTACTGCAATAAGAGGACCACATGGCGTAAAAAAACCGGCAGCTATATGACTCATATTTGGTTTTATTTGATTAGGATTATTAATGCCAGTATGTTGAGTATCTCTTATCCTTGTATTGATAATTGAAGTAAtatta                                                                  <  1:444099/141‑1 (MQ=255)
                                                                    aaaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCGTTATTTGGATTATCACTTATCGTTGTATTTATAATTGAATGAAtatta                                                                  >  2:496154/1‑141 (MQ=255)
                                                                    aaaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                                  >  1:591118/1‑141 (MQ=255)
                                                                        aTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtatata                                                              <  1:494199/141‑1 (MQ=255)
                                                                          aCTGAAATAAAAGTACCACATCGGGTAAAATAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATACCATTAGTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATAtt                                                            <  2:727833/141‑1 (MQ=255)
                                                                           cTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                           <  1:117864/141‑1 (MQ=255)
                                                                            tGCAGTAAAAGTATAACATCGCGTAAAAAAACCAGCATGTATAAAACTCATAATATGTTTTATTGTATTAGGATGATTAATGCCATTATTTGGTTTATTACTTAACCTAGTATTTATATTTGAATTAATATTTTGTATTaa                                                          >  2:857215/1‑141 (MQ=255)
                                                                            tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaa                                                          >  1:322564/1‑141 (MQ=255)
                                                                              cattAAAAGTAGCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAg                                                        <  2:255112/138‑1 (MQ=255)
                                                                              cAATAAAAGTACCACATCGCTTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGACATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAg                                                        <  2:43624/141‑1 (MQ=255)
                                                                                   aaaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgt                                                   <  1:364920/141‑1 (MQ=255)
                                                                                    aaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtc                                                  <  2:487142/141‑1 (MQ=255)
                                                                                     aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGGTTATCACTTATCCTTGTATTTATAATTGATTTAATATTATATATTAAAGAtcgtcg                                                 >  1:672594/1‑141 (MQ=255)
                                                                                     aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTCTCCTTCTAGATCGAGTTGAATTAATATTATATATTAAAGCtcgtcg                                                 >  1:181849/1‑141 (MQ=255)
                                                                                     aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtcg                                                 >  2:594939/1‑141 (MQ=255)
                                                                                        aCCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                                              <  2:777376/141‑1 (MQ=255)
                                                                                             aTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTCAAc                                         <  1:712066/141‑1 (MQ=255)
                                                                                               cgcgTAAAAAAACCAGCATCTATATCACTCATGATATGTTTTATTGTATTAGGATTATTAATACCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCTTGCTAAACaa                                       >  1:708945/1‑141 (MQ=255)
                                                                                               cgcgTAAAAAAACCAGCATCTATATCACTCATGATATGTTTTATTGTATTAGGATTATTAATACCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTAGTGCTAAACaa                                       >  1:709264/1‑141 (MQ=255)
                                                                                                gcgTAAAAAAACCAGCATCTATATCACTCATCATATGTTTAATTGTATTAGGACTATTAATGCCATTATTTGGATTATCACTTATACTAGTATTTATAATTGAATTAATATTATATGTTAAAGATCGTCGTGCTAAACaat                                      <  2:299735/141‑1 (MQ=255)
                                                                                                  gTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataa                                    >  2:82094/1‑141 (MQ=255)
                                                                                                  gTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGATAAACaataa                                    >  2:469785/1‑141 (MQ=255)
                                                                                                     aaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTGGTGCTAAACAATAATGc                                 >  2:806833/1‑141 (MQ=255)
                                                                                                       aaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAACCAATAATGAAc                               >  2:42960/1‑141 (MQ=255)
                                                                                                        aactcAGCCTCTATATCCCTCATAATCTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                              <  1:612005/137‑1 (MQ=255)
                                                                                                          aCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTa                            <  1:616500/141‑1 (MQ=255)
                                                                                                           ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAACCAATATTGCACTTaa                           >  2:125253/1‑141 (MQ=255)
                                                                                                               cATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtt                       <  1:399172/141‑1 (MQ=255)
                                                                                                               cATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATAATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtt                       >  1:566848/1‑141 (MQ=255)
                                                                                                               cATCTATATCACTCATAATATGTTTTATTCCACTAGGATTATTAATACCATCATTTGGACTATCCCTTTTCCTTGTCTACATTAATGAAGTAATATGATATATTAAAGAGCGTCGGGCCAAACAATAAGGCACTTAAAggt                       >  2:474567/1‑139 (MQ=255)
                                                                                                                aTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTGTTTGGATTATCACGTATCCTTGTATTTATCACGGACGTAACTTTAAATAGTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGatt                      >  2:696915/1‑141 (MQ=255)
                                                                                                                   tataTCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTCTACAATAATGCACTTAAAGTTTTGa                   >  1:664741/1‑141 (MQ=255)
                                                                                                                             ataataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGaaa         >  2:608703/1‑141 (MQ=255)
                                                                                                                                atatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGACCTGACGAAAttt      >  2:890070/1‑141 (MQ=255)
                                                                                                                                    gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGCTTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAATTTTTAAATGCTGAAATTTACaa  >  2:640962/1‑141 (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 < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑