Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,671,899	T→G	T88P (ACG→CCG)	pntA ←	Re/Si‑specific NAD(P)(+) transhydrogenase subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,671,899	0	T	G	100.0%	334.7 / NA	88	T88P (ACG→CCG)	pntA	Re/Si‑specific NAD(P)(+) transhydrogenase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (43/45);  total (43/45)

AGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTT  >  NZ_CP009273/1671812‑1671985                                                                                        |                                                                                       agTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTg                                                                                      >  2:1136802/1‑90 (MQ=255) agTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTg                                                                                      >  2:55899/1‑90 (MQ=255)  gTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGgtgt                                                                                     <  1:2045615/90‑1 (MQ=255)  gTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGgtgt                                                                                     <  1:542211/90‑1 (MQ=255)     cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc                                                                                  >  2:2645581/1‑90 (MQ=255)     cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc                                                                                  >  1:678622/1‑90 (MQ=255)     cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc                                                                                  <  1:3005254/90‑1 (MQ=255)     cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc                                                                                  >  2:376323/1‑90 (MQ=255)       tCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAg                                                                                >  1:385804/1‑90 (MQ=255)          ccATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGAt                                                                             <  1:55899/90‑1 (MQ=255)            aTCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTc                                                                           >  1:1292483/1‑90 (MQ=255)            aTCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTc                                                                           >  2:1664687/1‑90 (MQ=255)            aTCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTc                                                                           >  1:1923240/1‑90 (MQ=255)            aTCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTc                                                                           >  1:2160457/1‑90 (MQ=255)            aTCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTc                                                                           >  2:240172/1‑90 (MQ=255)                    cACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTc                                                                           >  1:2348287/1‑82 (MQ=255)                    cACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTc                                                                           <  2:2348287/82‑1 (MQ=255)                    cACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGc                                                                   <  1:1136802/90‑1 (MQ=255)                    cACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGc                                                                   <  2:1429423/90‑1 (MQ=255)                    cACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGc                                                                   >  1:907232/1‑90 (MQ=255)                      cgttacgttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCaa                                                                 <  2:2087815/90‑1 (MQ=255)                      cgttacgttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCaa                                                                 <  2:1595464/90‑1 (MQ=255)                          acgttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtc                                                             >  2:2840098/1‑90 (MQ=255)                          acgttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtc                                                             >  2:2644466/1‑90 (MQ=255)                          acgttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtc                                                             <  1:362467/90‑1 (MQ=255)                            gttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat                                                           >  1:568628/1‑90 (MQ=255)                            gttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat                                                           >  1:1733363/1‑90 (MQ=255)                            gttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat                                                           <  1:2740623/90‑1 (MQ=255)                            gttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat                                                           >  2:2057492/1‑90 (MQ=255)                            gttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat                                                           >  1:1900260/1‑90 (MQ=255)                            gttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat                                                           >  2:2695499/1‑90 (MQ=255)                             ttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcatc                                                          <  2:2623500/90‑1 (MQ=255)                             ttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcatc                                                          <  2:1476480/90‑1 (MQ=255)                              tCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc                                                                                  <  1:538668/65‑1 (MQ=255)                              tCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc                                                                                  >  2:538668/1‑65 (MQ=255)                                    aGTTTTTGCATTACTTCCGGCTTCCGACCCGGCTATATAAATCTCCCCCGGGGTGTTCTAGGCTTCAGTAACGCAATTTCATCATCTAAc                                                   <  1:2644466/90‑1 (MQ=255)                                     gTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACg                                                  <  2:2312590/90‑1 (MQ=255)                                      tttttGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACgg                                                 <  1:623215/90‑1 (MQ=255)                                      tttttGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACgg                                                 <  1:1381013/90‑1 (MQ=255)                                       ttttGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGgc                                                <  1:465120/90‑1 (MQ=255)                                         ttGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGgcgc                                              <  2:2160457/90‑1 (MQ=255)                                         ttGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGgcgc                                              >  2:1333156/1‑90 (MQ=255)                                           gCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCAt                                            <  2:651021/90‑1 (MQ=255)                                             aTTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTg                                          <  2:241145/90‑1 (MQ=255)                                             aTTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTg                                          <  2:1255357/90‑1 (MQ=255)                                              ttAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGa                                         >  1:2297408/1‑90 (MQ=255)                                              ttAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGa                                         >  2:2956836/1‑90 (MQ=255)                                                aaTTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGAcc                                       >  2:102754/1‑90 (MQ=255)                                                     cGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAg                                  >  2:1153718/1‑90 (MQ=255)                                                      ggATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGa                                 >  1:2161327/1‑90 (MQ=255)                                                       gATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGaa                                <  2:1484510/90‑1 (MQ=255)                                                        aTTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAAt                               <  1:1070654/90‑1 (MQ=255)                                                        aTTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAAt                               <  1:240172/90‑1 (MQ=255)                                                        aTTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAAt                               <  2:678622/90‑1 (MQ=255)                                                        aTTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAAt                               <  2:1945757/90‑1 (MQ=255)                                                           cTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc                                                                                  <  1:1411757/36‑1 (MQ=37)                                                           cTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc                                                                                  >  2:1411757/1‑36 (MQ=37)                                                           cTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCGTCATCTAACGGCGCATTGACCTTCAGAATGAt                            >  1:2195362/1‑90 (MQ=255)                                                            tGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc                                                                                  <  2:1651509/35‑1 (MQ=37)                                                            tGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc                                                                                  >  1:1651509/1‑35 (MQ=255)                                                            tGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGAtc                           >  2:343403/1‑90 (MQ=255)                                                            tGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGCAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGAtc                           <  1:1784454/90‑1 (MQ=255)                                                             gcgcAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGAtct                          >  1:543268/1‑90 (MQ=255)                                                                  ggCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGAc                     <  1:1873553/90‑1 (MQ=255)                                                                  ggCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGAc                     >  1:1926366/1‑90 (MQ=255)                                                                  ggCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGAc                     <  1:2645581/90‑1 (MQ=255)                                                                  ggCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGAc                     >  2:1422561/1‑90 (MQ=255)                                                                       gATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCa                <  1:652981/90‑1 (MQ=255)                                                                       gATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCa                >  2:2701902/1‑90 (MQ=255)                                                                       gATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCa                <  1:2796362/90‑1 (MQ=255)                                                                        aTAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAg               <  2:1733363/90‑1 (MQ=255)                                                                          aaaaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGAc             <  1:1391865/90‑1 (MQ=255)                                                                          aaaaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGAc             <  2:1432369/90‑1 (MQ=255)                                                                          aaaaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGAc             <  2:1516276/90‑1 (MQ=255)                                                                          aaaaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGAc             <  1:2042022/90‑1 (MQ=255)                                                                          aaaaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGAc             <  1:2265005/90‑1 (MQ=255)                                                                            aaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGc           >  2:2638856/1‑90 (MQ=255)                                                                            aaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGc           >  2:2482984/1‑90 (MQ=255)                                                                            aaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGc           <  2:1983368/90‑1 (MQ=255)                                                                            aaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGc           >  2:1983650/1‑90 (MQ=255)                                                                            aaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGc           >  2:2009890/1‑90 (MQ=255)                                                                               tccccAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTAt        <  1:3019867/87‑1 (MQ=255)                                                                               tCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTAt        <  1:1398725/90‑1 (MQ=255)                                                                                cACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCACAATGATCTCTGACTGCCAGACGCTAtt       >  1:1508328/1‑90 (MQ=255)                                                                                 aCCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGAc                     >  1:2867328/1‑75 (MQ=255)                                                                                 aCCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGAc                     <  2:2867328/75‑1 (MQ=255)                                                                                 aCCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTc      >  2:73960/1‑90 (MQ=255)                                                                                   cAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTccc    <  2:1720785/90‑1 (MQ=255)                                                                                     gCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAg               <  1:2305449/77‑1 (MQ=255)                                                                                     gCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCtt  >  1:1153722/1‑90 (MQ=255)                                                                                        |                                                                                       AGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTT  >  NZ_CP009273/1671812‑1671985

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑