Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,509,792 A→G 10.2% intergenic (‑104/‑266) 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_ALE2,509,7920AG10.2% 140.3 / 6.8 49intergenic (‑104/‑266)narT/USA300HOU_RS12920putative nitrate transporter NarT/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (28/16);  new base G (2/3);  total (30/19)
Fisher's exact test for biased strand distribution p-value = 3.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01

ATGTAAGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTAGACACTTA  >  USA300TCH1516_ALE/2509655‑2509926
                                                                                                                                         |                                                                                                                                      
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                                                                                                                  <  1:84928/141‑1 (MQ=255)
                   ttttgttttgTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTAtt                                                                                                                  >  1:128168/1‑141 (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                                                                            >  1:693795/1‑141 (MQ=255)
                                                         tttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGa                                                                            >  2:215906/1‑141 (MQ=255)
                                                         tttatttTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGa                                                                            >  1:633739/1‑141 (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                                                                  <  1:688290/141‑1 (MQ=255)
                                                                   aaTAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGAt                                                                  >  2:333558/1‑141 (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)
                                                                                                                                 atatGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTAGACACt    >  2:305370/1‑141 (MQ=255)
                                                                                                                                  tatGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTAGACACtt   >  1:395213/1‑141 (MQ=255)
                                                                                                                                   atGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTAGACACTTa  >  1:128112/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                      
ATGTAAGTTGAAAGCCACCTTTTGTTTTGTACATACGTTTCACCTTCATCAAAATCATTTATTTTTTAATAGATATCAATACTCTGCCTATATATTAGAGGTCAATGTTATTTAAAAATGCTTTCATTTATATGAAAACATTCAATATAGACAAAGTATTGACTACATATATATTTTATTATGATTGTGAAAAAGTGAACATAAGGATTTTCCCTTATTTATGAAGTGATTTACCCTATACAATGTCCCTTTAAGATGCTTTTAGACACTTA  >  USA300TCH1516_ALE/2509655‑2509926

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑