Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,509,782 T→A 10.2% intergenic (‑94/‑276) narT ← / → USA300HOU_RS12920 putative nitrate transporter NarT/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,509,7820TA10.2% 161.4 / 9.7 49intergenic (‑94/‑276)narT/USA300HOU_RS12920putative nitrate transporter NarT/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (26/18);  new base A (2/3);  total (28/21)
Fisher's exact test for biased strand distribution p-value = 6.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

TTTGTAATGTAAGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTA  >  USA300TCH1516_ALE/2509649‑2509918
                                                                                                                                     |                                                                                                                                        
tttGTAATGTAAGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGa                                                                                                                                   <  1:355212/141‑1 (MQ=255)
 ttGTAATGTAAGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGaa                                                                                                                                  <  2:96665/141‑1 (MQ=255)
  tgtaatgtaaGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCTTTTATATGaaa                                                                                                                                 >  1:434719/1‑141 (MQ=255)
      atgtaaGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGTTTTCATATAAATGAAAGCAt                                                                                                                             <  1:324213/141‑1 (MQ=255)
        gtaaGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCACCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTc                                                                                                                           >  2:195884/1‑141 (MQ=255)
          aaGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCaa                                                                                                                         >  1:489882/1‑141 (MQ=255)
           aGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGTTTTCATATAAATGAAAGCAttttta                                                                                                                        <  2:334023/141‑5 (MQ=255)
           aGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAat                                                                                                                        <  1:120062/141‑1 (MQ=255)
            gTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGTTTTCATATAAATGAAAGCAtttttaa                                                                                                                       <  1:633990/141‑6 (MQ=255)
                    ccACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACaaa                                                                                                               >  1:137131/1‑141 (MQ=255)
                    ccACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACaaa                                                                                                               >  1:137241/1‑141 (MQ=255)
                     cACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAg                                                                                                              >  1:519017/1‑141 (MQ=255)
                        cTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAt                                                                                                           >  2:23953/1‑141 (MQ=255)
                         ttttgttttgTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt                                                                                                          >  1:128168/1‑141 (MQ=255)
                         ttttgttttgTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt                                                                                                          <  1:84928/141‑1 (MQ=255)
                              ttttgtACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTa                                                                                                     >  1:559018/1‑141 (MQ=255)
                                    aCATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatata                                                                                               >  1:715857/1‑141 (MQ=255)
                                       tACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACatatatat                                                                                            <  1:774020/141‑1 (MQ=255)
                                                ccTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATg                                                                                   >  1:565246/1‑141 (MQ=255)
                                                   tcatcaAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGAtt                                                                                >  1:715359/1‑141 (MQ=255)
                                                        aaaaTCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTAAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGaa                                                                           >  1:313556/1‑141 (MQ=255)
                                                               tttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGa                                                                    >  2:215906/1‑141 (MQ=255)
                                                               tttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGa                                                                    >  1:633739/1‑141 (MQ=255)
                                                               tttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGa                                                                    >  1:693795/1‑141 (MQ=255)
                                                                   ttttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACAt                                                                >  2:16465/1‑141 (MQ=255)
                                                                    tttttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATa                                                               <  1:239318/141‑1 (MQ=255)
                                                                      tttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAg                                                             <  2:313541/141‑1 (MQ=255)
                                                                      tttAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAg                                                             >  1:219344/1‑141 (MQ=255)
                                                                         aaTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAt                                                          >  2:333558/1‑141 (MQ=255)
                                                                         aaTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAt                                                          <  1:688290/141‑1 (MQ=255)
                                                                            aGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAtttt                                                       <  1:516771/141‑1 (MQ=255)
                                                                              atatCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTcc                                                     >  1:500522/1‑141 (MQ=255)
                                                                                   aaTACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttat                                                >  1:643122/1‑141 (MQ=255)
                                                                                     tACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCttattt                                              <  1:451011/141‑1 (MQ=255)
                                                                                           gCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAg                                        <  2:152751/141‑1 (MQ=255)
                                                                                            ccTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGt                                       >  1:380133/1‑141 (MQ=255)
                                                                                                 atatTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGAttt                                  >  1:580702/1‑141 (MQ=255)
                                                                                                     tAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTAccc                              >  1:94484/1‑141 (MQ=255)
                                                                                                            cAATGTTATTTAAAAACTCTTTCATTTATATTAAAACATTCAATAAAGACAAAGTAATGACGACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACaa                       <  1:663528/141‑1 (MQ=255)
                                                                                                             aaTGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAAt                      <  1:513156/141‑1 (MQ=255)
                                                                                                                      tAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTa             <  2:151625/141‑1 (MQ=255)
                                                                                                                      tAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTa             >  1:770905/1‑141 (MQ=255)
                                                                                                                           aTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATg        <  1:281795/141‑1 (MQ=255)
                                                                                                                           aTGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATg        <  2:266271/141‑1 (MQ=255)
                                                                                                                             gCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCt      <  1:754804/141‑1 (MQ=255)
                                                                                                                              ttttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCtt     >  1:176525/2‑141 (MQ=255)
                                                                                                                              cTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCtt     >  1:142038/1‑141 (MQ=255)
                                                                                                                               tttCATATAAATGAAAGCATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCttt    >  2:222741/1‑141 (MQ=255)
                                                                                                                                 tCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTa  <  1:385391/141‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                        
TTTGTAATGTAAGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTA  >  USA300TCH1516_ALE/2509649‑2509918

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑