Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 707,909 A→T 100% M1M (TTG→ATG) † znuC_1 ← High‑affinity zinc uptake system ATP‑binding protein ZnuC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE707,9090AT100.0% 195.8 / NA 59M1M (TTG→ATG) †znuC_1High‑affinity zinc uptake system ATP‑binding protein ZnuC
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (33/26);  total (33/26)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGAA  >  USA300TCH1516_ALE/707773‑708045
                                                                                                                                        |                                                                                                                                        
ttGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGt                                                                                                                                      <  1:265282/141‑1 (MQ=255)
 tGATAAGGAAAGATTCACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGtt                                                                                                                                     <  2:342442/141‑1 (MQ=255)
         gAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATAcctc                                                                                                                             >  1:197335/1‑141 (MQ=255)
              tttACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAAt                                                                                                                        >  2:713290/1‑141 (MQ=255)
               ttcccAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAAtt                                                                                                                       <  1:67612/138‑1 (MQ=255)
               ttACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAAtt                                                                                                                       >  1:212735/1‑141 (MQ=255)
                tACCAGCACCATTCGGGCCCATGATACCAATTATTTCTCCGCGTACTGGGAGCGATGAGGAAGTGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATGTTTTGTTTCTAACATACGTTTATACCTCCTAATTa                                                                                                                      >  1:181842/1‑141 (MQ=255)
                tACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTa                                                                                                                      >  2:50881/1‑141 (MQ=255)
                     gCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGt                                                                                                                 <  2:197335/141‑1 (MQ=255)
                           ttCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTTTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGc                                                                                                           >  2:522552/1‑141 (MQ=255)
                              gggCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACCTGCTTATTCACTAAAAACAGCTAAAAATCTTTTGTTTCTAACATACGATTATACCTCCTAATTAAAAGTTTAGGCTaa                                                                                                        >  2:149637/1‑141 (MQ=255)
                              gggCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTaa                                                                                                        >  2:543687/1‑141 (MQ=255)
                                gCCCATGATACCAATTCTTTCGCGGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAGCAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAAcc                                                                                                      <  2:464750/141‑1 (MQ=255)
                                  ccATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCta                                                                                                    <  1:261767/141‑1 (MQ=255)
                                   cgtGATACCAATTATTTCGCCGCGTATTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTATACTAACCtaa                                                                                                   <  1:567464/139‑1 (MQ=255)
                                    aTGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCCAGCTGAAAGTTTAGGCTAACCtaat                                                                                                  <  2:748459/141‑1 (MQ=255)
                                     tGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCtaatt                                                                                                 <  1:634502/141‑1 (MQ=255)
                                        tACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCtaattaat                                                                                              <  1:664507/141‑1 (MQ=255)
                                         aCCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTaattaatt                                                                                             >  2:113478/1‑141 (MQ=255)
                                             attattTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGtat                                                                                         >  2:421683/1‑141 (MQ=255)
                                              ttattTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGtata                                                                                        <  1:75422/141‑1 (MQ=255)
                                                  ttCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTACCCTAATTAATTGTAtaataa                                                                                    >  1:308898/1‑141 (MQ=255)
                                                  ttCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATGTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTataatca                                                                                    >  1:117897/1‑139 (MQ=255)
                                                     gccgcGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACt                                                                                 >  1:504443/1‑141 (MQ=255)
                                                     gccgcGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACt                                                                                 >  1:390012/1‑141 (MQ=255)
                                                     gccgcGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACt                                                                                 <  1:67238/141‑1 (MQ=255)
                                                     gccgcGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTAATAACTAGAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACt                                                                                 <  2:351408/141‑1 (MQ=255)
                                                        gcgTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTgag                                                                              <  2:88957/141‑1 (MQ=255)
                                                              tGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATAtt                                                                        >  1:166009/1‑141 (MQ=255)
                                                              tGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGACCTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATAtt                                                                        >  1:214494/1‑141 (MQ=255)
                                                                  tttgATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATc                                                                    <  2:674974/138‑1 (MQ=255)
                                                                        aaGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCa                                                              >  1:747544/1‑141 (MQ=255)
                                                                         aGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCaa                                                             >  1:63578/1‑141 (MQ=255)
                                                                            aaaTGTTTTTAAGTACATGCTTTTTACCTAAAAACAGATTTAAATCTTTTAGTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATCATAACCTGAGAATCTTTATTATCTCAAGTa                                                          >  2:507310/1‑141 (MQ=255)
                                                                               tGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAAt                                                       <  1:692698/141‑1 (MQ=255)
                                                                                   tttAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGt                                                   <  2:555062/141‑1 (MQ=255)
                                                                                   tttAAGTACATGCTTACTACCTAAAAACAGATTTTAATCTATTGTTTCTATCATACGTTTAGGCCTCCTAATGAAAAGTTTAGGCTAACCTAAGTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGt                                                   <  2:448847/141‑1 (MQ=255)
                                                                                           caagCTTATAACCTAAAAACAGATTTAAATCTTTTCTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGatataat                                           <  2:56106/138‑1 (MQ=255)
                                                                                                      ccTAAAAACAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGTAAAAATATAGACAatgt                                >  2:731357/1‑141 (MQ=255)
                                                                                                         aaaaaCAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAatgtatg                             >  1:36789/1‑141 (MQ=255)
                                                                                                           aaaCAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTAtgtg                           <  2:592499/141‑1 (MQ=255)
                                                                                                             aCAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAg                         <  1:143717/141‑1 (MQ=255)
                                                                                                              cAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAgg                        <  2:212735/141‑1 (MQ=255)
                                                                                                              cAGATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAgg                        >  1:626390/1‑141 (MQ=255)
                                                                                                                gATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTg                      >  2:758867/1‑141 (MQ=255)
                                                                                                                gATTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTAGTAATATAATATAGACAATGTATGTGAgtgg                      >  2:167787/1‑138 (MQ=255)
                                                                                                                 aTTTAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTCATTAATTGTATAATAAACTGAGAGTATTTATCATGTCCAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGGGa                     >  1:650920/1‑141 (MQ=255)
                                                                                                                   ttAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGaaa                   >  1:179504/1‑141 (MQ=255)
                                                                                                                   ttAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACAGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAAATTATGTAAGGTGaaa                   >  2:662302/1‑141 (MQ=255)
                                                                                                                    tAAATCTTTTGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAg                  >  2:137447/1‑141 (MQ=255)
                                                                                                                             tGTTTTTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAAc         <  2:486213/141‑1 (MQ=255)
                                                                                                                             tGTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAAc         >  2:84418/1‑141 (MQ=255)
                                                                                                                              gTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACt        <  1:543687/141‑1 (MQ=255)
                                                                                                                              gTTTCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACt        >  1:230958/1‑141 (MQ=255)
                                                                                                                                ttCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTga      <  1:113478/141‑1 (MQ=255)
                                                                                                                                 tgtAACATACGTTTATAACTCCTACTTAAAAGTTTAGGCTAACGTAATTAATTATAGAATCAACTGAGAATATTTATTATGTCATGTAAAGTCCTGTTATAGTATAGACAACGTCAGTGGGGTGAAAGTATGTTAACTgaa     >  2:615014/3‑141 (MQ=255)
                                                                                                                                 tCTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaa     >  1:414191/1‑141 (MQ=255)
                                                                                                                                  cTAACATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaag    <  1:50881/141‑1 (MQ=255)
                                                                                                                                    aaCATACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaagaa  >  1:243028/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                        
TTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGAA  >  USA300TCH1516_ALE/707773‑708045

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: ‑