Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,535,733	A→C	F46V (TTT→GTT)	envZ ←	sensory histidine kinase EnvZ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,535,733	0	A	C	100.0%	301.0 / NA	82	F46V (TTT→GTT)	envZ	sensory histidine kinase EnvZ
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (36/46);  total (36/46)

GACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAAACTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTA  >  NC_000913/3535637‑3535827                                                                                                 |                                                                                               gACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACct                                                                                              <  1:2589441/99‑1 (MQ=255)   cGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACctgc                                                                                            <  2:897844/99‑1 (MQ=255)     gAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACctgctg                                                                                          <  2:1618059/99‑1 (MQ=255)     gAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACctgctg                                                                                          >  2:1964009/1‑99 (MQ=255)       aaGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGa                                                                                        >  2:323723/1‑99 (MQ=255)        aGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAg                                                                                       <  2:1036701/99‑1 (MQ=255)         gCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAgg                                                                                      >  2:1234935/1‑99 (MQ=255)           gggAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCt                                                                                    <  1:1430431/99‑1 (MQ=255)            ggAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTc                                                                                   <  2:784610/99‑1 (MQ=255)              aGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCgg                                                                                 >  2:956515/1‑99 (MQ=255)               ggCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGc                                                                                <  2:22075/99‑1 (MQ=255)               ggCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGc                                                                                >  1:1824644/1‑99 (MQ=255)                  acaACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCaaa                                                                             <  2:1967177/99‑1 (MQ=255)                   caaccaacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCaaaa                                                                            >  1:800324/1‑99 (MQ=255)                   caaccaacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCaaaa                                                                            >  1:1726550/1‑99 (MQ=255)                   caaccaacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCaaaa                                                                            <  2:1858047/99‑1 (MQ=255)                    aaccaacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAAt                                                                           <  2:95073/99‑1 (MQ=255)                    aaccaacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAAt                                                                           <  1:903878/99‑1 (MQ=255)                    aaccaacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAAt                                                                           <  1:192261/99‑1 (MQ=255)                      ccaacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATcg                                                                         >  2:2074352/1‑99 (MQ=255)                       caacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATcgc                                                                        >  2:2281744/1‑99 (MQ=255)                            gCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGt                                                                   <  2:486879/99‑1 (MQ=255)                            gCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGt                                                                   <  1:193200/99‑1 (MQ=255)                             cGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGtt                                                                  <  1:2452902/99‑1 (MQ=255)                              gTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTc                                                                 >  2:2105368/1‑99 (MQ=255)                                 ccGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGc                                                              <  2:830809/99‑1 (MQ=255)                                  cGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGca                                                             <  1:1616057/99‑1 (MQ=255)                                   gTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGcac                                                            <  2:1367954/99‑1 (MQ=255)                                     cctccAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGcacca                                                          >  2:1281767/1‑99 (MQ=255)                                      ctccAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGcaccac                                                         >  1:2095497/1‑99 (MQ=255)                                      ctccAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGcaccac                                                         <  1:1111433/99‑1 (MQ=255)                                         cAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAg                                                      >  2:1986520/1‑99 (MQ=255)                                          aGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGa                                                     <  2:77529/99‑1 (MQ=255)                                             tGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATaa                                                  >  2:1375498/1‑99 (MQ=255)                                              gCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAg                                                 >  2:1318479/1‑99 (MQ=255)                                                aGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAgtc                                               >  2:1465501/1‑99 (MQ=255)                                                  tttGTCGGTCATCAACATACGCACTTCGTACGCGAGGCCTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAgtcgt                                             >  1:2198473/1‑99 (MQ=255)                                                  tttGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAgtcgt                                             <  1:774518/99‑1 (MQ=255)                                                  tttGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAgtcgt                                             >  1:1688916/1‑99 (MQ=255)                                                   ttGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAgtcgtc                                            >  2:2157095/1‑99 (MQ=255)                                                   ttGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAgtcgtc                                            >  1:1053538/1‑99 (MQ=255)                                                    tGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCa                                           >  2:73899/1‑99 (MQ=255)                                                    tGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCa                                           <  2:2169647/99‑1 (MQ=255)                                                     gTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCAc                                          <  1:452569/99‑1 (MQ=255)                                                      tCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCAcc                                         >  1:1179286/1‑99 (MQ=255)                                                      tCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCAcc                                         >  2:376474/1‑99 (MQ=255)                                                      tCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCAcc                                         >  2:1998336/1‑99 (MQ=255)                                                       cGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCa                                        >  1:1311/1‑99 (MQ=255)                                                        ggTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAg                                       >  1:717742/1‑99 (MQ=255)                                                          tcatcaACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGc                                     <  1:1036557/99‑1 (MQ=255)                                                          tcatcaACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGc                                     >  1:342779/1‑99 (MQ=255)                                                          tcatcaACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGc                                     <  1:517670/99‑1 (MQ=255)                                                           catcaACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCt                                    <  2:2178538/99‑1 (MQ=255)                                                            atcaACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTg                                   <  1:1849301/99‑1 (MQ=255)                                                            atcaACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTg                                   >  1:1821180/1‑99 (MQ=255)                                                             tcaACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTgg                                  >  2:426111/1‑99 (MQ=255)                                                                 cATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGaa                              <  1:2001513/99‑1 (MQ=255)                                                                        aCTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAg                       >  1:74481/1‑99 (MQ=255)                                                                         cTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAgg                      <  2:1154010/99‑1 (MQ=255)                                                                         cTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAgg                      <  2:919746/99‑1 (MQ=255)                                                                          ttCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGt                     <  2:1479236/99‑1 (MQ=255)                                                                          ttCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGt                     <  1:165190/99‑1 (MQ=255)                                                                           tCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTg                    <  2:1701111/99‑1 (MQ=255)                                                                           tCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTg                    <  1:1320374/99‑1 (MQ=255)                                                                            cGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGa                   <  2:1199186/99‑1 (MQ=255)                                                                              tACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACg                 >  2:761290/1‑99 (MQ=255)                                                                               aCGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGa                <  2:1069212/99‑1 (MQ=255)                                                                               aCGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGa                <  1:1825923/99‑1 (MQ=255)                                                                               aCGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGa                <  1:1917177/99‑1 (MQ=255)                                                                                  cgAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGa             <  1:1452885/99‑1 (MQ=255)                                                                                  cgAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGa             <  1:2205229/99‑1 (MQ=255)                                                                                    aGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGc           >  1:1485747/1‑99 (MQ=255)                                                                                    aGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGc           >  1:1277594/1‑99 (MQ=255)                                                                                      gACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCaa         <  1:6758/99‑1 (MQ=255)                                                                                       aCTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAAt        >  2:185234/1‑99 (MQ=255)                                                                                          ttattaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAAc     <  1:330152/99‑1 (MQ=255)                                                                                           tattaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACg    >  1:2105909/1‑99 (MQ=255)                                                                                            attaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGt   >  1:1674795/1‑99 (MQ=255)                                                                                            attaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGt   <  2:1399740/99‑1 (MQ=255)                                                                                             ttaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTa  <  2:1974405/99‑1 (MQ=255)                                                                                             ttaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTa  <  2:1045454/99‑1 (MQ=255)                                                                                             ttaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTa  <  2:1565701/99‑1 (MQ=255)                                                                                                 |                                                                                               GACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAAACTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTA  >  NC_000913/3535637‑3535827

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑