Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,521,593	C→T	*295* (TAG→TAA)	xapR ←	transcriptional activator of xapAB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,521,593	0	C	T	100.0%	222.3 / NA	69	*295* (TAG→TAA)	xapR	transcriptional activator of xapAB
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (36/33);  total (36/33)

CACGACCCACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGT  >  NC_000913/2521473‑2521726                                                                                                                         |                                                                                                                                        cACGACCCACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGcc                                                                                                                     <  2:25139/139‑1 (MQ=255)      cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCaa                                                                                                                   <  2:259898/136‑1 (MQ=255)      cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCaa                                                                                                                   >  1:259898/1‑136 (MQ=255)      cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAg                                                                                                                >  1:863284/1‑139 (MQ=255)      cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAg                                                                                                                >  1:490319/1‑139 (MQ=255)              tGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTGTCAATGCAGCCAACAGCt                                                                                                              <  2:1390036/135‑1 (MQ=38)              tGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTGTCAATGCAGCCAACAGCt                                                                                                              >  1:1390036/1‑135 (MQ=255)                tAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATc                                                                                                      >  2:283841/1‑139 (MQ=255)                tAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATc                                                                                                      >  2:265510/1‑139 (MQ=255)                tAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATc                                                                                                      >  2:689647/1‑139 (MQ=255)                 aaaaaaGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                     <  1:283841/139‑1 (MQ=255)                      aGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                                <  2:311401/139‑1 (MQ=255)                        cggcgtAAAGGAGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                              >  2:961661/6‑139 (MQ=255)                        cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                              <  2:1288626/139‑1 (MQ=255)                        cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGACGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                              >  1:1147579/1‑139 (MQ=255)                          cccTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTc                                                                                             >  1:481094/1‑138 (MQ=255)                          cccTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTc                                                                                             <  2:481094/138‑1 (MQ=255)                                     cTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑tg                                                                                                                                  <  2:1221734/90‑1 (MQ=255)                                     cTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑tg                                                                                                                                  >  1:1221734/1‑90 (MQ=255)                                         tttGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                    >  2:1198598/1‑132 (MQ=255)                                         tttGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                    <  1:1198598/132‑1 (MQ=255)                                         tttGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCAt                                                                             <  1:961661/139‑1 (MQ=255)                                          ttGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATa                                                                            <  2:1042600/139‑1 (MQ=255)                                            gCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  1:265510/139‑1 (MQ=255)                                            gCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  2:490319/139‑1 (MQ=255)                                            gCTATCTGCGATTTGCGAAATTGCCTGACGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  2:1147579/139‑1 (MQ=255)                                                 cTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAata                                                                     <  1:689647/139‑1 (MQ=255)                                                  tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCAt                                                                             <  1:708920/130‑1 (MQ=255)                                                  tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCAt                                                                             >  2:708920/1‑130 (MQ=255)                                                  tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAatat                                                                    >  1:673952/1‑139 (MQ=255)                                                                 tGCCTGATGCGCTTCATTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGa                                                     <  1:2765/139‑1 (MQ=255)                                                                    cTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATgc                                                  >  2:239253/1‑139 (MQ=255)                                                                        tGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCAc                                                                                           <  1:597566/94‑1 (MQ=255)                                                                        tGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCAc                                                                                           >  2:597566/1‑94 (MQ=255)                                                                            cTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAc                                                                                                                                      >  2:1427077/1‑49 (MQ=255)                                                                            cTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAc                                                                                                                                      <  1:1427077/49‑1 (MQ=255)                                                                             ttCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCa                                                                                                                    >  1:1096441/1‑64 (MQ=255)                                                                             ttCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCa                                                                                                                    <  2:1096441/64‑1 (MQ=255)                                                                              tCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                                <  1:1178039/83‑1 (MQ=255)                                                                              tCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                                >  2:1178039/1‑83 (MQ=255)                                                                                    aGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAAtatata                                                                 >  2:498020/1‑108 (MQ=255)                                                                                    aGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAAtatata                                                                 <  1:498020/108‑1 (MQ=255)                                                                                      cAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGcggacgga                                <  1:239253/139‑1 (MQ=255)                                                                                         actactATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCa                                                                                            <  1:1007895/76‑1 (MQ=255)                                                                                         actactATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCa                                                                                            >  2:1007895/1‑76 (MQ=255)                                                                                         actactATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                        >  2:1605984/1‑96 (MQ=255)                                                                                         actactATTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                        <  1:1605984/96‑1 (MQ=255)                                                                                           tactaTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACctgct                                                                                      >  2:522215/1‑80 (MQ=255)                                                                                           tactaTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACctgct                                                                                      <  1:522215/80‑1 (MQ=255)                                                                                           tactaTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATg                           >  1:546491/1‑139 (MQ=255)                                                                                              taTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                    >  2:977975/1‑79 (MQ=255)                                                                                              taTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                    <  1:977975/79‑1 (MQ=255)                                                                                              taTTTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGaca                        >  1:1427732/1‑139 (MQ=255)                                                                                              taTCTCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGaca                        >  1:1380465/1‑139 (MQ=255)                                                                                                tttCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          >  2:466606/1‑87 (MQ=255)                                                                                                tttCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  1:466606/87‑1 (MQ=255)                                                                                                tttCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACAcc                      >  2:89237/1‑139 (MQ=255)                                                                                                  tCCGGCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTg                    <  2:863284/139‑1 (MQ=255)                                                                                                     ggCAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGcc                 >  2:616656/1‑139 (MQ=255)                                                                                                       cAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCa                                                                                                                    >  2:1345724/1‑38 (MQ=255)                                                                                                       cAATTCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCa                                                                                                                    <  1:1345724/38‑1 (MQ=255)                                                                                                          ttCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGcggacgg                                 <  1:1052672/118‑1 (MQ=255)                                                                                                          ttCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGcggacgg                                 >  2:1052672/1‑118 (MQ=255)                                                                                                          ttCCTGTCTCCTCACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTc            >  1:687240/1‑139 (MQ=255)                                                                                                                    ctcACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          >  2:641733/1‑67 (MQ=255)                                                                                                                    ctcACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  1:641733/67‑1 (MQ=255)                                                                                                                    ctcACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGt  >  2:1072105/1‑139 (MQ=255)                                                                                                                     tcACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATcgcg                                                                                                   >  1:942031/1‑41 (MQ=255)                                                                                                                     tcACTTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATcgcg                                                                                                   <  2:942031/41‑1 (MQ=255)                                                                                                                         |                                                                                                                                        CACGACCCACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTAC‑‑TGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGT  >  NC_000913/2521473‑2521726

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑