Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	209,716	T→C	I300T (ATC→ACC)	tilS →	tRNA lysidine(34) synthetase TilS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	209,716	0	T	C	100.0%	318.8 / NA	85	I300T (ATC→ACC)	tilS	tRNA lysidine(34) synthetase TilS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (51/34);  total (51/34)

GCGACGCGTTGGTGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAATCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGACGTGG  >  NZ_CP009273/209632‑209795                                                                                     |                                                                                gcgACGCGTTGGTGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGAc                                                                            >  2:1576086/1‑90 (MQ=255)   gACGCCTTGGTGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGc                                                                          <  1:2410740/90‑1 (MQ=255)      gcgTTGGTGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTAt                                                                       >  2:168432/1‑90 (MQ=255)        gTTGGTGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCa                                                                     <  2:915097/90‑1 (MQ=255)        gTTGGTGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCa                                                                     <  1:282089/90‑1 (MQ=255)        gTTGGTGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCa                                                                     <  1:45673/90‑1 (MQ=255)        gTTGGTGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCa                                                                     >  2:405842/1‑90 (MQ=255)           ggTGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTc                                                                  <  2:1579846/90‑1 (MQ=255)           ggTGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTc                                                                  <  2:226433/90‑1 (MQ=255)             tGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGc                                                                <  2:564643/90‑1 (MQ=255)              gAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCa                                                               <  2:34759/90‑1 (MQ=255)                ggATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAAc                                                             >  1:1301305/1‑90 (MQ=255)                ggATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAAc                                                             <  2:2281696/90‑1 (MQ=255)                 gATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACt                                                            >  2:2982659/1‑90 (MQ=255)                     tGGCAGGAAGTGGCGCTGGCGCGGGCAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGCCGCAACTgtgg                                                        <  2:324350/90‑1 (MQ=255)                     tGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGGGCGTTTGAAACCCGACGCTATCAGTCGCAACTgtgg                                                        >  1:324350/1‑90 (MQ=255)                     tGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCa                                                                     <  1:1436689/77‑1 (MQ=255)                     tGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCa                                                                     >  2:1436689/1‑77 (MQ=255)                     tGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTc                                                                  >  2:2323173/1‑80 (MQ=255)                     tGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTc                                                                  <  1:2323173/80‑1 (MQ=255)                     tGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTgtgg                                                        >  2:1721819/1‑90 (MQ=255)                     tGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTgtgg                                                        >  2:2729719/1‑90 (MQ=255)                     tGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTgtgg                                                        >  2:1417952/1‑90 (MQ=255)                     tGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTgtgg                                                        >  1:2961738/1‑90 (MQ=255)                     tGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTgtgg                                                        >  1:2958481/1‑90 (MQ=255)                      ggCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTgtggt                                                       <  1:1871828/90‑1 (MQ=255)                      ggCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTgtggt                                                       <  2:1611543/90‑1 (MQ=255)                      ggCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTgtggt                                                       <  2:2779333/90‑1 (MQ=255)                          ggAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGc                                                                          >  2:411260/1‑67 (MQ=255)                          ggAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGc                                                                          <  1:411260/67‑1 (MQ=255)                          ggAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGAt                                                   >  2:1790745/1‑90 (MQ=255)                          ggAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGAt                                                   >  2:683386/1‑90 (MQ=255)                          ggAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGAt                                                   <  1:1328004/90‑1 (MQ=255)                           gAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGAtt                                                  >  2:550736/1‑90 (MQ=255)                                    ctggcgcGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTc                                         >  1:339116/1‑90 (MQ=255)                                           gggAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCa                                                                     <  2:2652630/55‑1 (MQ=255)                                           gggAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCa                                                                     >  1:2652630/1‑55 (MQ=255)                                           gggAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGc                                  >  2:1181964/1‑90 (MQ=255)                                            ggAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCa                                 <  2:2474230/90‑1 (MQ=255)                                            ggAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCa                                 <  2:1256091/90‑1 (MQ=255)                                              aaGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCaaa                               <  2:603417/90‑1 (MQ=255)                                              aaGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCaaa                               <  2:1631311/90‑1 (MQ=255)                                                gATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTc                                                                  >  1:111061/1‑53 (MQ=255)                                                gATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTc                                                                  <  2:111061/53‑1 (MQ=255)                                                gATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGc                             >  2:2033353/1‑90 (MQ=255)                                                   gCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGaa                          <  1:1542213/90‑1 (MQ=255)                                                   gCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGaa                          <  1:2483547/90‑1 (MQ=255)                                                     cTCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGaaaa                        <  2:295207/90‑1 (MQ=255)                                                      tCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCaaa                               <  2:1944017/82‑1 (MQ=255)                                                      tCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCaaa                               >  1:1944017/1‑82 (MQ=255)                                                      tCACCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAAc                       >  2:41116/1‑90 (MQ=255)                                                        aCCCTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACAt                     <  1:1534818/90‑1 (MQ=255)                                                           cTGTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATtgt                  >  2:1227917/1‑90 (MQ=255)                                                             gTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGaaa                         >  1:1414975/1‑81 (MQ=255)                                                             gTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGaaa                         <  2:1414975/81‑1 (MQ=255)                                                             gTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGc                <  1:2033353/90‑1 (MQ=255)                                                             gTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGc                >  1:1075355/1‑90 (MQ=255)                                                             gTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGc                >  2:2039959/1‑90 (MQ=255)                                                             gTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGc                >  1:2475118/1‑90 (MQ=255)                                                             gTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGc                <  1:384949/90‑1 (MQ=255)                                                             gTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGc                >  2:2810761/1‑90 (MQ=255)                                                             gTTTACGTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGc                >  1:979265/1‑90 (MQ=255)                                                                   gTTTGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGc          <  2:979265/90‑1 (MQ=255)                                                                     ttGGGCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAg        >  1:1747031/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCa         >  2:1627347/1‑87 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCa         <  1:1627347/87‑1 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  2:2176554/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  1:1015321/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  1:1092316/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  2:808193/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  1:1349737/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  2:677035/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  1:2852211/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  1:325851/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  1:839857/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  1:964083/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  2:121260/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  2:1251588/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  2:2943299/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  2:1382565/1‑90 (MQ=255)                                                                       gggCGCGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGAc      >  2:2596265/1‑90 (MQ=255)                                                                         gcgcGTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGACGt    >  1:753989/1‑90 (MQ=255)                                                                           gcgTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGACGTgg  >  2:2794812/1‑90 (MQ=255)                                                                            cgTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATcc                                            <  1:2779204/47‑1 (MQ=255)                                                                            cgTTTGAAACCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATcc                                            >  2:2779204/1‑47 (MQ=255)                                                                                     |                                                                                GCGACGCGTTGGTGAGGATCTGGCAGGAAGTGGCGCTGGCGCGGGAAGATGCCTCACCCTGTTTACGTTTGGGCGCGTTTGAAATCCGACGCTATCAGTCGCAACTGTGGTGGATTAAATCCGTCACCGGGCAAAGCGAAAACATTGTGCCGTGGCAGACGTGG  >  NZ_CP009273/209632‑209795

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑