Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,965,782	T→G	E389D (GAA→GAC)	tar ←	methyl‑accepting chemotaxis protein II

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,965,782	0	T	G	100.0%	253.3 / NA	69	E389D (GAA→GAC)	tar	methyl‑accepting chemotaxis protein II
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (27/42);  total (27/42)

GAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATAA  >  NZ_CP009273/1965695‑1965864                                                                                        |                                                                                   gAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTc                                                                                  <  2:953148/90‑1 (MQ=255)    ggCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCAcc                                                                               >  2:80343/1‑90 (MQ=255)            tctcTTTTGCCGCCTGGGCGCTGCGACGGGCAAGATTACCCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcg                                                                       <  1:2880493/90‑1 (MQ=21)             ctctTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgc                                                                      <  2:633751/90‑1 (MQ=255)             ctctTTTGCCCCCGGGGCGCTGCGACTGGCAAGATTCCGCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgc                                                                      <  1:1355088/90‑1 (MQ=25)               ctTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCgg                                                                    >  1:1320498/1‑90 (MQ=255)                    gccgccTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCa                                                               >  2:1636665/1‑90 (MQ=255)                      cgccGGGGCGCTGCGACGGGCAAGATTCCCCCCTCCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAAc                                                             <  1:945765/90‑1 (MQ=21)                         cTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGGCACCCGCACGCGCGGCTTCAACcgc                                                          >  1:1299217/1‑90 (MQ=255)                           gggCGCTGGGCCGGGCAGGATTACGCTCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCgg                                                        <  1:80343/90‑1 (MQ=18)                           gggCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcg                                                                       <  1:2883172/75‑1 (MQ=255)                           gggCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcg                                                                       >  2:2883172/1‑75 (MQ=255)                           gggCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCgg                                                        >  2:1154029/1‑90 (MQ=255)                                cTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTc                                                   >  1:641820/1‑90 (MQ=255)                                cTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTc                                                   <  2:835455/90‑1 (MQ=255)                                cTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTc                                                   >  2:874644/1‑90 (MQ=255)                                cTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTc                                                   <  2:947735/90‑1 (MQ=255)                                cTGCGACGGGCAAGATTACCCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTc                                                   <  1:896839/90‑1 (MQ=255)                                      cTGGCAAGATTACGCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGcgcg                                             <  1:2019655/90‑1 (MQ=255)                                        ggCAAGATTCCGCCCTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAg                                           <  2:684695/90‑1 (MQ=37)                                        ggCAAGATTCCCCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAg                                           <  1:2868073/90‑1 (MQ=37)                                        ggCAAGATTACGCCCTCCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAg                                           <  1:681482/90‑1 (MQ=37)                                        ggCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAg                                           <  2:684694/90‑1 (MQ=255)                                            aGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCCGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGaaa                                       >  2:2174020/1‑88 (MQ=255)                                             gATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGatat                                      <  2:2864316/90‑1 (MQ=255)                                             gATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGatat                                      <  2:2410433/90‑1 (MQ=255)                                              aTTACGCGTTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATAtt                                     <  2:104997/90‑1 (MQ=37)                                                tccGCACTCCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAg                                   <  1:1350112/88‑1 (MQ=255)                                                   gcccTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAAc                                                             <  1:2367879/58‑1 (MQ=255)                                                   gCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAAc                                                             >  2:2367879/1‑61 (MQ=255)                                                     cctacACCCGCCACCACGGCAAAAACCCGGCCCTGGTCACCCGCACCCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTgg                              <  1:2174020/86‑1 (MQ=255)                                                     aCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTgg                              <  2:1789257/90‑1 (MQ=255)                                                     aCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTgg                              <  1:1061998/90‑1 (MQ=255)                                                      cTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGa                             >  2:1386670/1‑90 (MQ=255)                                                       ttCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGcgcg                                             <  2:1397177/73‑1 (MQ=255)                                                       ttCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGcgcg                                             >  1:1397177/1‑73 (MQ=255)                                                       ttCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGaa                            >  2:316013/1‑90 (MQ=255)                                                       ttCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGaa                            >  1:1881715/1‑90 (MQ=255)                                                       ttCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGaa                            >  2:1649322/1‑90 (MQ=255)                                                        tcccccGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTgg                              <  2:2569582/84‑1 (MQ=255)                                                        tCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTgg                              >  1:2569582/1‑87 (MQ=255)                                                        tCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAg                           >  1:879285/1‑90 (MQ=255)                                                        ccccccGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAg                           <  1:1882464/87‑1 (MQ=255)                                                           cccGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCa                        >  2:476997/1‑90 (MQ=255)                                                           cccGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCa                        >  1:2146619/1‑90 (MQ=255)                                                            ccGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCaa                       <  1:316013/90‑1 (MQ=255)                                                             cGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAAt                      >  2:2154087/1‑90 (MQ=255)                                                              gCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcg                                                                       >  1:1632161/1‑40 (MQ=255)                                                              gCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcg                                                                       <  2:1632161/40‑1 (MQ=255)                                                              gCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATa                     >  2:1398839/1‑90 (MQ=255)                                                                 accacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCg                  <  2:306796/90‑1 (MQ=255)                                                                 accacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCg                  <  1:1126369/90‑1 (MQ=255)                                                                 accacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCg                  <  2:2275994/90‑1 (MQ=255)                                                                  ccacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTgg                              <  2:2112053/77‑1 (MQ=255)                                                                  ccacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTgg                              >  1:2112053/1‑77 (MQ=255)                                                                  ccacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGt                 >  2:2472944/1‑90 (MQ=255)                                                                     cGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGa              >  2:2564938/1‑90 (MQ=255)                                                                      ggCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGAt             <  2:2176759/90‑1 (MQ=255)                                                                       gCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATa            <  2:486736/90‑1 (MQ=255)                                                                       gCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATa            <  2:2442456/90‑1 (MQ=255)                                                                         aaaaCCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAAc          <  2:2146619/90‑1 (MQ=255)                                                                         aaaaCCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAAc          <  1:336051/90‑1 (MQ=255)                                                                         aaaaCCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAAc          <  1:2437967/90‑1 (MQ=255)                                                                         aaaaCCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAAc          <  2:18007/90‑1 (MQ=255)                                                                         aaaaCCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAAc          <  1:1636665/90‑1 (MQ=255)                                                                         aaaaCCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAAc          <  1:789817/90‑1 (MQ=255)                                                                           aaCCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGc        <  1:1642425/90‑1 (MQ=255)                                                                               aCGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAt    >  2:1649491/1‑90 (MQ=255)                                                                                 ggCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATaa  >  2:1184649/1‑90 (MQ=255)                                                                                        |                                                                                   GAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATAA  >  NZ_CP009273/1965695‑1965864

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑