Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,962,341 G→T M555I (ATG→ATT)  rep → ATP‑dependent DNA helicase Rep

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,962,3410GT75.9% 100.4 / 43.7 54M555I (ATG→ATT) repATP‑dependent DNA helicase Rep
Reads supporting (aligned to +/- strand):  ref base G (7/6);  new base T (18/23);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 7.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATGACGGAGATGCTGGAAGGCAGTGAACTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGATAATATCGATGAGGAGCGGCGGCTGGCCTATGTCGGCATTAC  >  NC_000913/3962209‑3962478
                                                                                                                                    |                                                                                                                                         
gATGACGGAGATGCTGGAAGGCAGTGAACTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCGACTGATTACTCTcc                                                                                                                                    >  1:230030/1‑140 (MQ=255)
gATGACGGAGATGCTGGAAGGCAGTGAACTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGC‑TTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCa                                                                                                                                   >  2:361953/1‑140 (MQ=255)
  tGACGGAGATGCTGGAAGGCAGTGAACTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCAc                                                                                                                                  <  2:644605/140‑1 (MQ=255)
  tGACGGAGATGCTGGAAGGCAGTGAACTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCAc                                                                                                                                  >  1:254120/1‑140 (MQ=255)
         aaTGCTGGAAGGCAGTGAACTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCACGCGTCGa                                                                                                                           <  1:608748/139‑1 (MQ=255)
          aTGCTGGAAGGCAGTGAACTGGATGAGCCGATGACGCTCACCCGGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGaa                                                                                                                          <  1:29904/140‑1 (MQ=255)
               ggAAGGCAGTGAACTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGc                                                                                                                     <  2:101770/140‑1 (MQ=255)
                gAAGGCAGTGAACTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGCCGAAAGGGCt                                                                                                                    >  1:375849/1‑140 (MQ=255)
                      aGTGAACTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGtt                                                                                                              >  2:562192/1‑140 (MQ=255)
                        tGAACTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTc                                                                                                            >  1:409201/1‑140 (MQ=255)
                          aaCTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCt                                                                                                          <  2:127214/140‑1 (MQ=255)
                          aaCTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCt                                                                                                          >  1:36852/1‑140 (MQ=255)
                            cTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTa                                                                                                        <  2:740771/140‑1 (MQ=255)
                             tGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTAt                                                                                                       >  1:180703/1‑140 (MQ=255)
                                    gCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACa                                                                                                >  2:248004/1‑140 (MQ=255)
                                    gCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACa                                                                                                >  2:513940/1‑140 (MQ=255)
                                     ccGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACAt                                                                                               >  2:161208/1‑140 (MQ=255)
                                        aTGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGt                                                                                            <  1:634614/140‑1 (MQ=255)
                                        aTGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGt                                                                                            <  2:364875/140‑1 (MQ=255)
                                        aTGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGt                                                                                            <  1:252477/140‑1 (MQ=255)
                                        aTGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGt                                                                                            <  1:731400/140‑1 (MQ=255)
                                        aTGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGt                                                                                            <  2:238724/140‑1 (MQ=255)
                                        aTGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGt                                                                                            <  1:408325/140‑1 (MQ=255)
                                        aTGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGt                                                                                            <  2:527144/140‑1 (MQ=255)
                                         tGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCt                                                                                                          <  1:197128/125‑1 (MQ=255)
                                         tGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCt                                                                                                          >  2:197128/1‑125 (MQ=255)
                                                         ggtgACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGt                                                                           >  2:632950/1‑140 (MQ=255)
                                                             aCGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGttttt                                                                       >  1:191183/1‑140 (MQ=255)
                                                               gcgcTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGc                                                                     <  1:161208/140‑1 (MQ=255)
                                                               gcgcTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGc                                                                     <  2:708229/140‑1 (MQ=255)
                                                               gcgcTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGc                                                                     <  1:603757/140‑1 (MQ=255)
                                                                cgcTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGcc                                                                    >  1:695828/1‑140 (MQ=255)
                                                                 gcTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCg                                                                   >  1:555106/1‑140 (MQ=255)
                                                                  cTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGc                                                                  <  2:191183/140‑1 (MQ=255)
                                                                    ttACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCAc                                                                <  2:36852/140‑1 (MQ=255)
                                                                     tACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCAcc                                                               >  2:136775/1‑140 (MQ=255)
                                                                         ttGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCagag                                                           <  1:711513/140‑1 (MQ=255)
                                                                         ttGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCagag                                                           <  2:51711/140‑1 (MQ=255)
                                                                             gcgACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGagcagc                                                       >  1:310778/1‑140 (MQ=255)
                                                                              cgACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCGACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAgcagca                                                      <  2:230030/140‑1 (MQ=255)
                                                                              cgACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAgcagca                                                      <  2:17407/140‑1 (MQ=255)
                                                                              cgACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAgcagca                                                      <  2:555106/140‑1 (MQ=255)
                                                                                 aatgatgGGGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCACGCGTCGAAAGCGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCg                                                   <  2:720688/139‑1 (MQ=255)
                                                                                           cGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGataa                                         >  1:8326/1‑140 (MQ=255)
                                                                                             tggtgAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGataata                                       >  1:309951/1‑140 (MQ=255)
                                                                                                tgAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGATAATATCg                                    >  2:377244/1‑140 (MQ=255)
                                                                                                             gagCTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGATAATATCGATGAGGAgcggcg                       <  2:664033/140‑1 (MQ=255)
                                                                                                                cTGGATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGATAATATCGATGAGGAGCGGCGGCt                    >  1:458951/1‑140 (MQ=255)
                                                                                                                   gATCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGATAATATCGATGAGGAGCGGCGGCTGGc                 <  2:695828/140‑1 (MQ=255)
                                                                                                                   gATCAGGTGCAACTGATGACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGATAATATCGATGAGGAGCGGCGGCTGGc                 >  2:305360/1‑140 (MQ=255)
                                                                                                                    aTCAGGTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGATAATATCGATGAGGAGCGGCGGCTGGcc                >  1:64166/1‑140 (MQ=255)
                                                                                                                        ggTGCAACTGATTACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCTGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGATAATATCGATGAGGAGCGGCGGCTGGCCTATg            >  1:687859/1‑140 (MQ=255)
                                                                                                                        ggTGCAACTGATGACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGTCGCACCAGAGCAGCATCGATGAAGATAATATCGATGAGGAGCGGCGGCTGGCCTATg            <  1:513940/140‑1 (MQ=255)
                                                                                                                        ggTGCAACTGATGACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGATAATATCGATGAGGAGCGGCGGCTGGCCTATg            <  1:361953/140‑1 (MQ=255)
                                                                                                                                  atgaCTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGATAATATCGATGAGGAGCGGCGGCTGGCCTATGTCGGCATTAc  >  1:517168/1‑140 (MQ=255)
                                                                                                                                    |                                                                                                                                         
GATGACGGAGATGCTGGAAGGCAGTGAACTGGATGAGCCGATGACGCTCACCCAGGTGGTGACGCGCTTTACTTTGCGCGACATGATGGAGCGTGGTGAGAGTGAAGAAGAGCTGGATCAGGTGCAACTGATGACTCTCCACGCGTCGAAAGGGCTGGAGTTTCCTTATGTCTACATGGTCGGTATGGAAGAAGGGTTTTTGCCGCACCAGAGCAGCATCGATGAAGATAATATCGATGAGGAGCGGCGGCTGGCCTATGTCGGCATTAC  >  NC_000913/3962209‑3962478

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑