Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 707,879 A→T 100% L11I (TTA→ATA)  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_ALE707,8790AT99.0% 167.9 / ‑6.4 56L11I (TTA→ATA) znuC_1High‑affinity zinc uptake system ATP‑binding protein ZnuC
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base T (33/21);  total (34/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGGTAGCATTAAATTCACCAATTAAAGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATG  >  USA300TCH1516_ALE/707744‑708014
                                                                                                                                       |                                                                                                                                       
cGGTAGCATTAAATTCACCAATTAAAGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACa                                                                                                                                    >  2:498317/1‑141 (MQ=255)
       aTTAAATTCACCAATTAAAGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTATTCAAGTACATGCTTATTACCTATAAACAGATTTaa                                                                                                                             >  1:494636/1‑141 (MQ=255)
        ttAAATTCACCAATTAAAGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTaaa                                                                                                                            >  1:535354/1‑141 (MQ=255)
        ttAAATTCACCAATTAAAGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTaaa                                                                                                                            >  1:535360/1‑141 (MQ=255)
           aaTTCACCAATTAAAGACTTGATAAGGGAAGATTTACCAGCACCATTCGGACCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACGTGCTTATTACCTATAAACAGATTTAAATCt                                                                                                                         >  2:413543/1‑141 (MQ=255)
              tCACCAATTAAAGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCtttt                                                                                                                      >  2:167350/1‑141 (MQ=255)
                 ccAATTAAGGCCTTGATAAGGGAAGGTTTACTCGCACCAGTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCCATAAACAGATTTAAATCTTTTGtt                                                                                                                   <  2:232052/141‑1 (MQ=255)
                         aGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACaa                                                                                                           >  1:44471/1‑141 (MQ=255)
                             ttGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTACTAAACGt                                                                                                       >  2:132515/1‑141 (MQ=255)
                             ttGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGt                                                                                                       >  2:265836/1‑141 (MQ=255)
                                aTAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTta                                                                                                    >  1:309356/1‑141 (MQ=255)
                                aTAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTta                                                                                                    >  1:249765/1‑141 (MQ=255)
                                aTAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTta                                                                                                    >  1:499935/1‑141 (MQ=255)
                                aTAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACAGGTATCGATACGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATCTACACCTTTTGTTTCTACCAAACgctca                                                                                                    >  2:106942/1‑137 (MQ=255)
                                 tAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTtat                                                                                                   <  1:339337/141‑1 (MQ=255)
                                       aaGATTTAGCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTTCTGGTATCGATGAGTGTATGGTTTTAAGTACATGGTTATTACCTCTAAACAGATTTAAATCTTTTGTTTCGAACCAGCGTTTATtcctcc                                                                                             <  2:141879/141‑1 (MQ=255)
                                       aaGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATAcctcc                                                                                             <  2:294213/141‑1 (MQ=255)
                                        aGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATAcctcct                                                                                            >  2:368479/1‑141 (MQ=255)
                                          aTTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTaa                                                                                          <  1:356935/141‑1 (MQ=255)
                                          aTTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTaa                                                                                          <  1:66514/141‑1 (MQ=255)
                                                cAGTACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGGTTTTAAGTACATGCTTATTACCTATGAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAAtttaca                                                                                    >  1:403381/1‑137 (MQ=255)
                                                    cccATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACCTGCTTATTACCTATAAACAGACTTAACTCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGttt                                                                                <  2:141563/140‑1 (MQ=255)
                                                         tCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCt                                                                           >  1:488896/1‑141 (MQ=255)
                                                          cGGGCCCCTGAAACCAATTATTTCGCCGCGTACTGGGATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTGACATCTTTTGTTTCTAGCAAACGTTTATACATCCTACTTAAAGATTTCGGCTa                                                                          >  2:427340/1‑141 (MQ=255)
                                                          cGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTa                                                                          >  1:283567/1‑141 (MQ=255)
                                                             gCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAAcc                                                                       >  1:247962/1‑141 (MQ=255)
                                                             gCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAAcc                                                                       <  1:380754/141‑1 (MQ=255)
                                                                           ttattTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGtata                                                         <  2:548238/141‑1 (MQ=255)
                                                                           tgtgttCGGCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGtata                                                         <  2:251274/137‑1 (MQ=255)
                                                                            ttttgcgccgcGTTCTGGTATCTATAAGGAAATGTTTTTAAGTACATGCTGATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTataa                                                        <  2:496107/136‑1 (MQ=255)
                                                                            tattTCGGCGCGCGCTGGTATAGAGAAGGAAGGGTTTTTAAGTACATGCTTATTACGTATACATAGATTGGAATTTTTTGTTTCTAACAAACGGTTATACCCCCTACTTAAATATTTTGGCTAACCTCATTAATAGTataa                                                        >  2:184451/1‑141 (MQ=255)
                                                                                  gccgcGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACt                                                  >  1:260989/1‑141 (MQ=255)
                                                                                   ccgcGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTg                                                 >  2:527844/1‑141 (MQ=255)
                                                                                    cgcgTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTga                                                >  1:471405/1‑141 (MQ=255)
                                                                                    cgcgTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTga                                                >  1:532786/1‑141 (MQ=255)
                                                                                      cgTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTgaga                                              <  1:401880/141‑1 (MQ=255)
                                                                                      cgTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTgaga                                              <  1:401967/141‑1 (MQ=255)
                                                                                          cTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAatat                                          <  2:560759/141‑1 (MQ=255)
                                                                                           tGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATAtt                                         >  1:457944/1‑141 (MQ=255)
                                                                                                    tAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTc                                >  2:210126/1‑141 (MQ=255)
                                                                                                    tAAGGAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTc                                >  2:210273/1‑141 (MQ=255)
                                                                                                       ggAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAg                             <  2:112415/141‑1 (MQ=255)
                                                                                                       ggAAATGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAg                             <  1:265836/141‑1 (MQ=255)
                                                                                                         aaaTGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTa                           >  2:408837/1‑141 (MQ=255)
                                                                                                            tGTTTTTAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAAt                        >  2:239357/1‑141 (MQ=255)
                                                                                                            cttgtgtAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAAt                        <  1:547345/135‑1 (MQ=255)
                                                                                                              tttttAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTc                      <  1:314837/141‑1 (MQ=255)
                                                                                                              tttttAAGTACATGCTTATTACCTATAAACAGATTTAAAACTTTTAATTCAATCAAACTTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTc                      <  1:16243/141‑1 (MQ=255)
                                                                                                                 ttAAGTACATGCTCATTACCTAAAAAAAGATTCAAATCGTTTGTTTATAACAAACGTTTATACCTCCTAATTAAAAGTCTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTg                   <  1:100704/141‑1 (MQ=255)
                                                                                                                  tAAGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGa                  >  1:51720/1‑141 (MQ=255)
                                                                                                                   aaGTACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGat                 <  2:488896/141‑1 (MQ=255)
                                                                                                                      tACATGCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGatata              >  1:171654/1‑141 (MQ=255)
                                                                                                                           gCTTATTACCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGatataatata         <  1:484378/141‑1 (MQ=255)
                                                                                                                                  aCCTATAAACAGATTTAAATCTTTTGTTTCTGACAAACGTTTATACCTCCCAATTAAAAGTTTAGGCTAACCTTATTAATTGTAGTATAAACTGCGGATATTGATCCTGTCAAGTACATTCGTGAGCAAATGTAGGCAatg  >  2:1076/1‑141 (MQ=255)
                                                                                                                                  aCCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAatg  >  1:547194/1‑141 (MQ=255)
                                                                                                                                  aCCTATAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAatg  >  1:262830/1‑141 (MQ=255)
                                                                                                                                       |                                                                                                                                       
CGGTAGCATTAAATTCACCAATTAAAGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATG  >  USA300TCH1516_ALE/707744‑708014

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑