Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,530,133 T→A 11.5% intergenic (‑196/+99) zinT ← / ← yoeB Metal‑binding protein ZinT/Toxin YoeB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,530,1330TA11.5% 136.1 / 4.4 55intergenic (‑196/+99)zinT/yoeBMetal‑binding protein ZinT/Toxin YoeB
Reads supporting (aligned to +/- strand):  ref base T (30/18);  new base A (2/5);  total (32/23)
Fisher's exact test for biased strand distribution p-value = 1.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAGCACTGTTTTTATAAATAATATAAAGTCGAATCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATGGTATTTACATGATGCTATTTTTATATGAT  >  USA300TCH1516_ALE/2530000‑2530269
                                                                                                                                     |                                                                                                                                        
cAAGCACTGTTTTTATAAATAATATAAAGTCGAATCATACTTTAGGTATTTACCAATTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTATGAACGTCATAATATAAGaag                                                                                                                                    >  2:514772/1‑139 (MQ=255)
  agaaCTGTTTTTATAAATAATATAAAGTCGAATCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTAATAATaaaaaaaaaa                                                                                                                                  <  2:286336/137‑1 (MQ=255)
      cTGTTTTTATAAATAATATAAAGTCGAATCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGa                                                                                                                              <  1:232561/140‑1 (MQ=255)
      cTGTTTTTAGAAATAATATAAAGTCCAATCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGa                                                                                                                              <  2:421804/140‑1 (MQ=255)
           tttATAAATAATATAAAGTAGAATCATACTTTAGGTATTTACCAGTTTTCATTTTATCTAATAGATGAATATTTTAAAAATATGATAAATAAAACTTTATAGTATTTACGAAAGTCATAATATAAGAAAAAAAGACactg                                                                                                                         >  2:137864/1‑137 (MQ=255)
            ttATAAATAATATAAAGTCGAATCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTTTTTAGGAAAGTCATAAAAAAAGAAAAAAAGACaaatt                                                                                                                        >  2:409070/1‑137 (MQ=255)
            ttATAAATAATATAAAGTCGAATCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAAtct                                                                                                                        >  1:473062/1‑140 (MQ=255)
               taaataaTATAAATGCGAATAATACTTTAGTTATTTAGCACTTTTCGTTTTAGCTAATACATGACTATTGTACAAATATGATCCAGAAACCTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTa                                                                                                                     <  2:185640/140‑1 (MQ=255)
               taaataaTATAAAGTCGAATCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTa                                                                                                                     <  2:38454/140‑1 (MQ=255)
               taaataaTATAAAGTCGAATCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTa                                                                                                                     <  2:36604/140‑1 (MQ=255)
                aaataaTATAAAGTCGAATCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTAt                                                                                                                    <  1:507544/140‑1 (MQ=255)
                         aaaGTCGAATCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATAATATTGCt                                                                                                           >  1:419539/1‑140 (MQ=255)
                              cccattaTACTTTAGGTATTTAACATTTGTCGTTTAAAAAAATACATGACTATTGTACAAATATAATACAAAAAAATTTATAGTATTTACGAACGTCAAAAAAAAAAAAAAAAAGACAATCTCTATCATATTGCTAATAg                                                                                                      <  2:477067/134‑1 (MQ=255)
                                  ttaTACTTTAGTTATTTACCACTTTTCATATTATCTAAGAAATGACCATTGTACAAATAAGATACAGAAAACTTTATAGTATTTACGAACGTAAAAAAAAAAAAAAAAAAGACAATCTCTATCATATTGCTAATAGAAAt                                                                                                  <  2:59188/138‑1 (MQ=255)
                                  tCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATATAAAt                                                                                                  >  1:403195/1‑140 (MQ=255)
                                     tACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGc                                                                                               >  2:429723/1‑140 (MQ=255)
                                      aCTTTAGGTATTTATCACTTTTCGGTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGcc                                                                                              <  2:495314/140‑1 (MQ=255)
                                      aCTTTAGGTATTTACCACTTTTCGTTTTGTCTAATACATGACTATTGTACAAATATGGTTCAGAATACTTTATAGTATTTGCGAACTTCCTAATATGAGAAAAAAAGACAATCTTTATCATATTCCTAATAGAAATTGcc                                                                                              >  2:233/1‑140 (MQ=255)
                                      aCTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATCCAGAAAACTTTATAGTATTTACGAACGTCATAATAAAAGAACAAACGACTATTTATATCATATTGCTAATCGaaagcaga                                                                                              >  1:208168/1‑135 (MQ=255)
                                         ttAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTCTTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAACAGAAATTGCCttt                                                                                           >  1:392612/1‑140 (MQ=255)
                                               aTTTACCACTTTTCGTTTTATCTAATACATGACTATTGTAAAAATATGAGACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGATAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCaaat                                                                                     >  2:334685/1‑140 (MQ=255)
                                                tttACCACTTTTCGTTTTATCTAATACATGACTCTTATCCAAATATGATAAAGAAAACGGTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATAtt                                                                                    >  1:541684/1‑140 (MQ=38)
                                                 ttACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTCTCGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCTTAttt                                                                                   >  2:381747/1‑139 (MQ=255)
                                                    cctgttttCGTTTTATCTAATAAATGAAAATTGTAATAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATAAAAAAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTcc                                                                                <  1:186276/136‑1 (MQ=37)
                                                    ccACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGACAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTcc                                                                                >  2:404960/1‑140 (MQ=255)
                                                    ccACTTTTCGATTTATCTAATACATGACAATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAACGACAATATCTATCATATTGCTAATAGAAATTGCATTTCCATATAGTcc                                                                                >  2:161214/1‑140 (MQ=255)
                                                     cACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCt                                                                               <  2:154478/140‑1 (MQ=255)
                                                      aCTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACCGAAAACTTTATAGTATTTACGAACGTCATAATATAAAAAAAAAAGACAATCTCTATCATATTACTAATAGAAATTGCCTTTTCATATTGTCCTa                                                                              >  1:221911/1‑140 (MQ=255)
                                                      aCTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGACAACTTTATAGTATTTACGAACGTCATAATATAAGAACAAAAGACAATCTCTATCATATTGCTAATAGAACTTGCCTTTTCATATTTTCCTa                                                                              >  2:433798/1‑140 (MQ=255)
                                                      aCTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTa                                                                              >  1:134458/1‑140 (MQ=255)
                                                      aCTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTa                                                                              >  2:85802/1‑140 (MQ=255)
                                                         tttCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACCATATTTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTaaaa                                                                           <  1:517712/140‑1 (MQ=255)
                                                           tCGTTTTATGTAATAAATGACTATTGTACAAGCATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAACAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATa                                                                         <  2:307395/140‑1 (MQ=38)
                                                             gTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAAc                                                                       <  2:391933/140‑1 (MQ=255)
                                                                      aaTACATGACTAATGCATGAAAATGAAACACAAAACTTTAGTGGATTTACGATCTTTATAAAATAAAAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCTTAAAATAACTTACCCTAt                                                              <  2:306182/140‑1 (MQ=21)
                                                                      aaTACAAGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTAt                                                              <  2:418835/140‑1 (MQ=255)
                                                                                    gTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGAc                                                >  2:9315/1‑140 (MQ=255)
                                                                                      aCAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATAATGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACtt                                              >  1:372259/1‑140 (MQ=255)
                                                                                         aaTATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCACTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGTCTTTTa                                           >  1:276692/1‑140 (MQ=255)
                                                                                              gATACAGAAAACTTTTTAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGAttt                                      >  1:408785/1‑140 (MQ=255)
                                                                                               aTACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTACTAAAATAACTTACCCTATTTTTATAGTGTGACTTATAGATTta                                     >  2:24916/1‑140 (MQ=255)
                                                                                               aTACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATAATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTta                                     >  2:471576/1‑140 (MQ=255)
                                                                                                     aaaaCTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATg                               >  2:531252/1‑140 (MQ=255)
                                                                                                          tttATAGTATTTACGAACGTCATAATATAATAAAAAAAGACAATCTCTTTCATAGTGCTAATAGAAATTGCCTTTTCATATTGTCCGAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATGGTAtt                          <  2:519814/140‑1 (MQ=255)
                                                                                                          tttATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATGATAtt                          >  1:184465/1‑140 (MQ=255)
                                                                                                          tttATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGACTTTTCATATTATCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATAGTAtt                          >  1:184392/1‑140 (MQ=255)
                                                                                                           ttATAGTATTTACGAACGTCATAATAAAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTACTAATGGTActt                         <  2:421297/140‑1 (MQ=255)
                                                                                                              taGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTTTGACTTTTAGATTTAATAATGGTATTTACa                      >  1:32422/1‑140 (MQ=255)
                                                                                                                  aTTTACGAACGTCATAATATAAGAAAAAAAGACAATCCCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATGGTATTTACatgat                  <  2:18188/140‑1 (MQ=255)
                                                                                                                    ttaacaaCCTCATAATATAAGAAAAAAATACAATCTTTATCATATTTCTAATAGAAATTTCCTTTTCATTTTTTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATGGTATTTACATGATGc                <  1:137864/135‑1 (MQ=255)
                                                                                                                     tACGAACGTCATAATATAAGAAAAAGAGACAATGTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATTACTTAGCCTATTTGTATAGTGTGACTTTTAGATTTAACAATGGTATTTACATGATGCt               <  1:334685/140‑1 (MQ=38)
                                                                                                                         aaCGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATGGTATTTACATGATGCTAttt           >  2:256915/1‑140 (MQ=255)
                                                                                                                          gcttCATAAAAAAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATGGTATTTACATGATGCTAtttt          <  2:218815/137‑1 (MQ=255)
                                                                                                                              cATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTATTCAAAATGACCAAAAATAACTTACCCAATTTTTATAGTGTGACTTTTAGATTTAATAATGGTATTTACATGATGCTATTTTtata      >  1:168878/1‑140 (MQ=38)
                                                                                                                               ataataTAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATGGTATTTACATGATGCTATTTTTatat     <  2:246888/140‑1 (MQ=255)
                                                                                                                               acaaaataAGAAAAAAAGACAAACTCAATCATATTGCTAATAGAAATTGCCGTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATGGTATTTACATGATGCTATTTTTatat     <  2:247067/135‑1 (MQ=255)
                                                                                                                                 aataTAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATGATGTGACTTTTAGATTTAATAATGGTATTTACATGATGCTATTTTTATATGa   >  2:109645/1‑140 (MQ=255)
                                                                                                                                  atatAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATGGTATTTACATGATGCTATTTTTATATGAt  <  2:134458/140‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                        
CAAGCACTGTTTTTATAAATAATATAAAGTCGAATCATACTTTAGGTATTTACCACTTTTCGTTTTATCTAATACATGACTATTGTACAAATATGATACAGAAAACTTTATAGTATTTACGAACGTCATAATATAAGAAAAAAAGACAATCTCTATCATATTGCTAATAGAAATTGCCTTTTCATATTGTCCTAAAATAACTTACCCTATTTTTATAGTGTGACTTTTAGATTTAATAATGGTATTTACATGATGCTATTTTTATATGAT  >  USA300TCH1516_ALE/2530000‑2530269

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: ‑