BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,873,627	Δ1 bp	coding (506/672 nt)	yidX →	putative replicase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,873,625	0	G	.	99.1%	515.0 / ‑2.2	117	coding (504/672 nt)	yidX	putative replicase
Reads supporting (aligned to +/- strand): ref base G (0/1); new base . (72/42); total (72/45)
Fisher's exact test for biased strand distribution p-value = 3.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 127 total aligned reads displayed.

TTACTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCGGGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCAATTTC  >  NC_000913/3873550‑3873696

ttACTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCg                                                                         >  2:2628729/1‑76 (MQ=255)

 tACTCAAAGCTGATGGCGTTCTACCATCCATCTAAAGTGCGCTTTTATGAATACTCTTCCCCCAGAGCCACTCCgg                                                                        <  2:5062109/76‑1 (MQ=255)

   cTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCggat                                                                      >  2:2526729/1‑74 (MQ=255)

   cTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCggat                                                                      <  2:5799413/76‑3 (MQ=255)

   cTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCggat                                                                      >  2:5610885/1‑74 (MQ=255)

    tCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCggatg                                                                     >  1:1032009/1‑73 (MQ=255)

    tCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCggatg                                                                     >  2:5051606/1‑73 (MQ=255)

    tCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATGCACCCAGAGGCATTCCggatg                                                                     >  2:5104145/1‑73 (MQ=255)

      aaaGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGgt                                                                  >  1:369252/1‑76 (MQ=255)

       aaGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGgtg                                                                 >  1:1795695/1‑76 (MQ=255)

        aGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGgtgt                                                                >  1:4140190/1‑76 (MQ=255)

        aGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGgtgt                                                                >  1:2801963/1‑76 (MQ=255)

         ggTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGtt                                                               >  2:5638731/1‑76 (MQ=255)

         ggTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGtt                                                               >  2:3273154/1‑76 (MQ=255)

          gTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGttt                                                              <  2:4761740/76‑1 (MQ=255)

           tGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTc                                                             <  2:3955707/76‑1 (MQ=255)

           tGATGGCATTCTACCATCCATTTAAAGTGCGATTTGATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTc                                                             <  1:1674353/76‑1 (MQ=255)

            gATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTcc                                                            <  1:4470310/76‑1 (MQ=255)

            gATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTcc                                                            >  2:2733408/1‑76 (MQ=255)

               ggCGTTCTACCATCCCTTTAAAGTGCGCTTTTATGAATCCTATTCACCCAGAGGCATTCC‑TGATTGTGTTTCCgca                                                         >  1:2196250/1‑76 (MQ=255)

               ggCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgca                                                         >  1:2153480/1‑76 (MQ=255)

                gCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcag                                                        <  2:447450/76‑1 (MQ=255)

                gCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcag                                                        >  1:2445388/1‑76 (MQ=255)

                 cGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcagc                                                       <  2:4669173/76‑1 (MQ=255)

                 cGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcagc                                                       >  1:2428917/1‑76 (MQ=255)

                  gTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcagca                                                      <  2:3241132/76‑1 (MQ=255)

                  gTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcagca                                                      >  2:873595/1‑76 (MQ=255)

                   ttCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCAt                                                     <  1:2510910/76‑1 (MQ=255)

                   ttCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCAt                                                     >  2:656074/1‑76 (MQ=255)

                   ttCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCAt                                                     <  2:2031135/76‑1 (MQ=255)

                     cTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTa                                                   >  2:1649954/1‑76 (MQ=255)

                     cTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTa                                                   <  1:2640576/76‑1 (MQ=255)

                       aCCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACt                                                 <  2:3600594/76‑1 (MQ=255)

                        ccatccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTg                                                >  2:3994178/1‑76 (MQ=255)

                         catccatTTAAAGTGCGATTTTATGTATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGc                                               >  2:1111144/1‑76 (MQ=255)

                         catccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGc                                               >  1:403645/1‑76 (MQ=255)

                           tccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCACTACTGCCa                                             >  1:5317877/1‑76 (MQ=255)

                            ccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAg                                            >  2:2053009/1‑76 (MQ=255)

                            ccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAg                                            >  1:2782666/1‑76 (MQ=255)

                            ccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAg                                            <  1:342084/76‑1 (MQ=255)

                            ccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAg                                            >  2:1404459/1‑76 (MQ=255)

                             catTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGt                                           >  2:2439166/1‑76 (MQ=255)

                             catTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGt                                           <  2:2741433/76‑1 (MQ=255)

                              atTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTg                                          >  2:1027122/1‑76 (MQ=255)

                              atTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTg                                          >  2:5766014/1‑76 (MQ=255)

                               tttAAAGTGGGATTTTATGAATACTATTCACCCAGAGGCATT‑CAGGATGGGGTTTCCGCAGCATTACTGCCAGTGa                                         <  2:420042/76‑1 (MQ=255)

                               nttAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGa                                         >  1:1939114/2‑76 (MQ=255)

                                ttAAAGTGCGATTTTATGAATATTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGAc                                        >  2:4235851/1‑76 (MQ=255)

                                ttAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGAc                                        >  2:361691/1‑76 (MQ=255)

                                ttAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGAc                                        >  1:1273184/1‑76 (MQ=255)

                                  aaaGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTg                                      >  2:1373955/1‑76 (MQ=255)

                                   aaGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGt                                     <  2:3441432/76‑1 (MQ=255)

                                    aGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGtt                                    >  1:960075/1‑76 (MQ=255)

                                     gTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTa                                   >  2:2707751/1‑76 (MQ=255)

                                     gTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTa                                   >  2:622693/1‑76 (MQ=255)

                                      ggCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTAc                                  <  2:1903011/75‑1 (MQ=255)

                                       gCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACg                                 >  2:1553408/1‑76 (MQ=255)

                                       gCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACg                                 >  1:5176703/1‑76 (MQ=255)

                                        cGATTTTCTGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGc                                >  2:3556800/1‑76 (MQ=255)

                                        cGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGc                                >  1:881242/1‑76 (MQ=255)

                                        cGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGc                                >  2:5625071/1‑76 (MQ=255)

                                          tttttATGAGTCCTATTCGCCGAGAGGCATTCC‑GAATGGTGTTTCCGCACCATTACTGCCAGTGACTGTTACGCTg                              <  1:5667220/75‑1 (MQ=255)

                                           ttttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTgg                             <  2:415260/76‑1 (MQ=255)

                                           ttttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTgg                             >  2:1770/1‑76 (MQ=255)

                                            tttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGa                            >  2:2048821/1‑76 (MQ=255)

                                            tttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGa                            >  1:1875489/1‑76 (MQ=255)

                                            tttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGAACGTTACGCTGGa                            >  2:5274683/1‑76 (MQ=255)

                                            tttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCCCAGCATTACTGCCAGTGACTGTTACGCTggc                            >  2:899007/1‑75 (MQ=255)

                                             ttATGAATATTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGAc                           <  1:4235852/76‑1 (MQ=255)

                                             ttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGAc                           <  1:1010495/76‑1 (MQ=255)

                                             ttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGAc                           >  1:3278976/1‑76 (MQ=255)

                                              tATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGAca                          >  2:3968493/1‑76 (MQ=255)

                                                  aaTACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGAcctcat                      >  2:5748158/1‑76 (MQ=255)

                                                   atccTATCCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCAtt                     <  1:13634/73‑1 (MQ=255)

                                                   aTACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCAtt                     <  1:1572884/76‑1 (MQ=255)

                                                    tACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTa                    >  2:5713539/1‑76 (MQ=255)

                                                    tACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTa                    >  2:546204/1‑76 (MQ=255)

                                                     aCTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTAc                   >  1:68244/1‑76 (MQ=255)

                                                      cTAGTCCCCCAGAGGCATTCCGGG‑TGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACt                  <  2:5591430/76‑1 (MQ=255)

                                                       tATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTg                 <  1:3817337/76‑1 (MQ=255)

                                                        aTTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGc                <  1:656074/76‑1 (MQ=255)

                                                        aTTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGc                >  1:1741270/1‑76 (MQ=255)

                                                         ttCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCa               >  1:4673337/1‑76 (MQ=255)

                                                          tCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCAc              <  2:2445388/76‑1 (MQ=255)

                                                          tCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCAc              >  1:2107380/1‑76 (MQ=255)

                                                          tCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTAATGCAc              >  1:5542833/1‑76 (MQ=255)

                                                           cACCCAGAGGCATTCC‑GTATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCAcc             <  1:4995732/76‑1 (MQ=255)

                                                            aCCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCg            <  2:3452068/76‑1 (MQ=255)

                                                             cccAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGc           >  1:4810644/1‑76 (MQ=255)

                                                              ccAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCt          >  2:1262265/1‑76 (MQ=255)

                                                              ccAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCt          >  2:3738085/1‑76 (MQ=255)

                                                               cAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACCTCATTACTGCACCCCTg         >  2:5686785/1‑76 (MQ=255)

                                                               cAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTg         >  2:4264629/1‑76 (MQ=255)

                                                                agagGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGc        >  1:1689137/1‑76 (MQ=255)

                                                                agagGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGc        <  1:4414206/76‑1 (MQ=255)

                                                                agagGCATTCC‑GGATGGTGTTTCCGCAGCATCACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGc        <  1:1770/76‑1 (MQ=255)

                                                                  agGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCaa      >  2:4508590/1‑76 (MQ=255)

                                                                   ggCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCAAt     >  1:3499279/1‑76 (MQ=255)

                                                                    gCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCAAtt    <  1:4141670/76‑1 (MQ=255)

                                                                      catCCCGGATGGTGTTTCCCCAGCATTCCTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCAAttt   <  1:899007/74‑1 (MQ=255)

TTACTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCGGGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCAATTTC  >  NC_000913/3873550‑3873696

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`