Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,499,437 T→A 6.8% V256D (GTT→GAT)  ypdA → sensory histidine kinase YpdA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,499,4370TA 6.8% 159.3 / 2.3 58V256D (GTT→GAT) ypdAsensory histidine kinase YpdA
Reads supporting (aligned to +/- strand):  ref base T (30/24);  new base A (2/2);  total (32/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.13e-01

ATATCGCCAACAAAACGCTACCGCTGTTTCGCCATGTCAATAGCGAGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCACCGCACACCAGAGATTCATTCCATGCTGG  >  NC_000913/2499302‑2499574
                                                                                                                                       |                                                                                                                                         
atatCGCCAACAAAACGCTACCGCTGTTTCGCCATGTAAATCGCGAGTCATTACGCAAGGTCTGCGAAATTATCCGCGAGGATGTTCACGCCGATGCGGGGGCCATTGCTGATACCGCTCATGCCGTGGCCGACGTTGGCGTg                                                                                                                                    >  2:171884/1‑143 (MQ=255)
       caacaaAACGCTACCGCTGTTTCGCCATGTCAATAGCGAGTCATTACGCACGGTCTGCGCAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGCAc                                                                                                                             >  2:11364/1‑143 (MQ=255)
          caaAACGCTACCGCTGTTTCGCCATGTCAATAGCGAGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATa                                                                                                                          <  1:850624/143‑1 (MQ=255)
           aaaaCGCTACCGCTGTTTCGCCATGTCAATAGCGAGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATTGGCTGGCCCAGGTTGGCGGGGGTGAACATaa                                                                                                                         >  2:545321/1‑143 (MQ=255)
                      gCTGTTTCGCCATGTCAATAGCGAGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGCTTACTAATACCGATCATCTGCTGGCCTATCTTTGCGGGGGTGAACATAACTATCAGAATg                                                                                                              >  2:379064/1‑143 (MQ=255)
                       tcgTTTCGCCATGTCAATAGCGAGCCACTACGCAAGGCCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATgg                                                                                                             <  1:556665/141‑1 (MQ=255)
                       cTGTCTCGCCAGGTCAATAGCGAGTCATTACGCAAGGTCGGCGAAACTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATgg                                                                                                             <  1:556682/143‑1 (MQ=255)
                           tgcGCCATGTCAATAGCGAGTCGTTACGCAAGGTCTGCGAAACTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTACTACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGAt                                                                                                         <  1:636561/141‑1 (MQ=255)
                             cGCCATGTCAATAGCGAGTCATTACGCAAGGTCTGCGACATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGa                                                                                                       <  1:515449/143‑1 (MQ=255)
                               ccATGTCAATAGCGAGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACt                                                                                                     >  1:291827/1‑143 (MQ=255)
                                cATGTCAATAGCGAGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACtt                                                                                                    >  1:763143/1‑143 (MQ=255)
                                       aTAGCGAGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCGTTAGc                                                                                             >  2:916672/1‑143 (MQ=255)
                                         aGCGAGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAGTACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCCGAGCGGCGATGACTTCATTAGccc                                                                                           >  2:757492/1‑143 (MQ=255)
                                            gAGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGAc                                                                                        >  2:430655/1‑143 (MQ=255)
                                             aGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACt                                                                                       >  1:86259/1‑143 (MQ=255)
                                             aGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACt                                                                                       >  1:579262/1‑143 (MQ=255)
                                               tCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACTGATCATGTGCTGGCCTATGTTGGCGTAGGAGAACATAACTAGAAGAATGGCGATGACTTCATTAGCCCGACTaa                                                                                     >  1:897285/1‑142 (MQ=255)
                                                     cGCAACGCCTGCGAACTTATCCGCGCTGACATTCACGCCGATGCGGTCGCGATTACTAATACCGATCATGTGCTGCCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCa                                                                               <  1:995298/143‑1 (MQ=255)
                                                             cTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGa                                                                       <  2:203250/143‑1 (MQ=255)
                                                              tGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATACCTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGaa                                                                      >  1:377709/1‑143 (MQ=255)
                                                               gCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAAt                                                                     >  1:983956/1‑143 (MQ=255)
                                                                cGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAAtt                                                                    >  1:715134/1‑143 (MQ=255)
                                                                 gAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATaa                                                                                                                         >  1:992951/1‑89 (MQ=255)
                                                                 gAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATaa                                                                                                                         <  2:1003298/89‑1 (MQ=255)
                                                                 gAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATaa                                                                                                                         <  2:992951/89‑1 (MQ=255)
                                                                 gAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATaa                                                                                                                         >  1:1003298/1‑89 (MQ=255)
                                                                 gAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGATGGCGTGGGTGAACATaa                                                                                                                         <  2:992958/89‑1 (MQ=255)
                                                                 gAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGATGGCGTGGGTGAACATaa                                                                                                                         >  1:992962/1‑89 (MQ=255)
                                                                 gAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGATGGCGTGGGTGAACATaa                                                                                                                         >  1:992958/1‑89 (MQ=255)
                                                                 gAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGATGGCGTGGGTGAACATaa                                                                                                                         <  2:992962/89‑1 (MQ=255)
                                                                  aaaTTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTAc                                                                  <  1:511856/143‑1 (MQ=255)
                                                                         ccGCGATGAGATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGaaaaa                                                           <  1:552713/143‑1 (MQ=255)
                                                                            cgAGGACATGCACGCCGGTGCGGTGGCGATTACTAATACCGATCATGTGCTGGCATATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAatca                                                        <  2:223848/143‑1 (MQ=255)
                                                                             gATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAatcat                                                       <  1:256019/143‑1 (MQ=255)
                                                                             gATGACACTCACGCCGATGCGGTGGCGCTTACTAATACCGATCATGTGCTGGCCTATTTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCTGTCAGGCGATGAATTACGGAAAAatcat                                                       <  1:877998/143‑1 (MQ=255)
                                                                              aTGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAatcatc                                                      >  1:976446/1‑143 (MQ=255)
                                                                              aTGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACATCATTAGCCCGACTACCCGTCAGGCCATGAACTACGGAAAAatcatc                                                      >  2:73333/1‑143 (MQ=255)
                                                                                aaCATCCACGCCGATGCGGTGGCGATTACTAACACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGCACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATcatcat                                                    <  2:911914/142‑1 (MQ=255)
                                                                                   agtggcGCCGGTGCGGTGGCGATTACTAATACCGATCATGTGCTGGGCTAGGTTGGCGTGGGTGCACATAACGATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTaa                                                 <  2:67990/138‑1 (MQ=255)
                                                                                   aTTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTaa                                                 >  2:930650/1‑143 (MQ=255)
                                                                                     tCACGCGGATGCGGTGGCGATTACTAATACCGGTCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTaaaa                                               <  2:369533/143‑1 (MQ=255)
                                                                                         gcccgtGCGGTGGCGCTTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACaa                                           <  2:955495/138‑1 (MQ=255)
                                                                                          ccGATGCGGTGGCGATTACTAATACGGATCAGGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGGTGACTTCATTAGCCCGGCTACCCGTCAGGCGATGAATTACGGAAAAATCATGATTAAAcacact                                          >  1:410484/1‑141 (MQ=255)
                                                                                            gATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAatga                                        >  2:227284/1‑143 (MQ=255)
                                                                                              tGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAatgatg                                      <  1:824383/143‑1 (MQ=255)
                                                                                                      cGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCAc                              <  2:377709/143‑1 (MQ=255)
                                                                                                       gATTACTAACACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCAcc                             <  1:53274/143‑1 (MQ=255)
                                                                                                             tAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCGGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAGCAATGATGAAGCCCACCGCacac                       >  1:152665/1‑143 (MQ=255)
                                                                                                             tAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCACCGcaccc                       >  1:16025/1‑141 (MQ=255)
                                                                                                             tAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCACCGCacac                       >  1:457128/1‑143 (MQ=255)
                                                                                                                  ccGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCACCGCACACCagag                  >  1:593547/1‑143 (MQ=255)
                                                                                                                    gATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCGCACCGCAAACCAGAGat                >  1:925440/1‑143 (MQ=255)
                                                                                                                    gATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCACCGCACACCAGAGat                >  1:498963/1‑143 (MQ=255)
                                                                                                                    gATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCACCGCACACCAGAGat                <  1:930650/143‑1 (MQ=255)
                                                                                                                     aTCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCACCGCACACCAGAGatt               <  2:225404/143‑1 (MQ=255)
                                                                                                                             cTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCACCGCACACCAGAGATTCATTCCAt       >  2:537687/1‑143 (MQ=255)
                                                                                                                              taggcTAAGTTGGCGTGGGTGAACATAACGATCAGAATGGCGATGAGTTCATTAGCCCGCCCAACCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCACCGCACACCAGAGATTCATTCCATg      <  2:250984/139‑1 (MQ=255)
                                                                                                                                  cTATGTTGGCGTGGGTGAACCTAACTATCAGAGTGGCGATGACTTCATTAGGCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCACCGCACACCAGAGATTCATTCCATGCTgg  >  2:532275/1‑143 (MQ=255)
                                                                                                                                       |                                                                                                                                         
ATATCGCCAACAAAACGCTACCGCTGTTTCGCCATGTCAATAGCGAGTCATTACGCAAGGTCTGCGAAATTATCCGCGATGACATTCACGCCGATGCGGTGGCGATTACTAATACCGATCATGTGCTGGCCTATGTTGGCGTGGGTGAACATAACTATCAGAATGGCGATGACTTCATTAGCCCGACTACCCGTCAGGCGATGAATTACGGAAAAATCATCATTAAAAACAATGATGAAGCCCACCGCACACCAGAGATTCATTCCATGCTGG  >  NC_000913/2499302‑2499574

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑