Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,013,868	A→G	N101D (AAC→GAC)	fliM →	flagellar motor switch protein FliM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,013,868	0	A	G	100.0%	129.3 / NA	37	N101D (AAC→GAC)	fliM	flagellar motor switch protein FliM
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (16/21);  total (16/21)

TGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCACCGAGTCTGGTGTTTATCGCCGTGGATAA  >  NZ_CP009273/2013782‑2013953                                                                                       |                                                                                      tgctgcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCgaccgacc                                                                                    <  2:2418280/90‑1 (MQ=255) tgctgcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCgaccgacc                                                                                    >  1:1756115/1‑90 (MQ=255) tgctgcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCAGTACCATGAATTTGCCCGCAACCTGCCGGTGCCgaccgacc                                                                                    <  2:843818/90‑1 (MQ=255)  gctgcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCt                                                                                   <  2:1153272/90‑1 (MQ=255)  gctgcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCt                                                                                   <  2:1230695/90‑1 (MQ=255)  gctgcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCt                                                                                   <  2:305986/90‑1 (MQ=255)  gctgcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCt                                                                                   <  2:1756115/90‑1 (MQ=255)   ctgcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTg                                                                                  <  1:1069103/90‑1 (MQ=255)      cgtcgtAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAAc                                                                               >  2:1435027/1‑90 (MQ=255)               ccGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCt                                                                                   <  2:2022054/77‑1 (MQ=255)               ccGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCt                                                                                   >  1:2022054/1‑77 (MQ=255)               ccGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTg                                                                                  >  2:1534442/1‑78 (MQ=255)               ccGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTg                                                                                  <  1:1534442/78‑1 (MQ=255)                     ataACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGaaa                                                                >  1:1768637/1‑90 (MQ=255)                     ataACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGaaa                                                                >  1:637965/1‑90 (MQ=255)                       aaCCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAAcc                                                              >  1:544907/1‑90 (MQ=255)                         ccGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGc                                                            <  2:1696974/90‑1 (MQ=255)                          cGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTACCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCt                                                           >  1:698786/1‑90 (MQ=255)                            tCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTTCCgaccgacc                                                                                    >  1:1167554/1‑63 (MQ=255)                            tCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTTCCgaccgacc                                                                                    <  2:1167554/63‑1 (MQ=255)                            tCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTgc                                                         >  1:1967332/1‑90 (MQ=255)                              ggggCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTgcgc                                                       <  1:1435027/90‑1 (MQ=255)                                   cATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCAc                                                  >  1:763355/1‑90 (MQ=255)                                    aTCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACt                                                 <  2:1967332/90‑1 (MQ=255)                                    aTCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACt                                                 <  2:898709/90‑1 (MQ=255)                                    aTCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACt                                                 <  1:1291572/90‑1 (MQ=255)                                         cATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCt                                            <  2:544907/90‑1 (MQ=255)                                               gCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACt                                                 <  1:102193/79‑1 (MQ=255)                                               gCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACt                                                 >  2:102193/1‑79 (MQ=255)                                               gCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTggtggt                                      >  1:1508669/1‑90 (MQ=255)                                                   tcccATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTtc                                  <  2:72401/88‑1 (MQ=255)                                                           aTTTGCCCGCACCCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGATGGTGGTGTTCTCACCGAg                          <  1:1321756/90‑1 (MQ=255)                                                            tttGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGc                                                    <  1:1915302/63‑1 (MQ=255)                                                            tttGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGc                                                    >  2:1915302/1‑63 (MQ=255)                                                                   gCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCACCGAGTCTgg                     <  1:2285985/87‑1 (MQ=255)                                                                   gCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCACCGAGTCTgg                     >  2:2285985/1‑87 (MQ=255)                                                                    cAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCACCGAGTCTGGTGtt                 >  1:522265/1‑90 (MQ=255)                                                                       ccTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCACCGAGTCTGGTGTTTAt              <  1:383841/90‑1 (MQ=255)                                                                           ccGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCACCGAGTCTGGTGTTTATCGcc          <  1:2351713/90‑1 (MQ=255)                                                                                gCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACt                                                 >  1:2276995/1‑46 (MQ=255)                                                                                gCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACt                                                 <  2:2276995/46‑1 (MQ=255)                                                                                gCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCACCGAGTCTGGTGTTTATCGCCGTGGa     >  1:711044/1‑90 (MQ=255)                                                                                  cgaccgacCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCACCGAGTCTGGTGTTTATCGCCGTGGATa   <  2:1508669/90‑1 (MQ=255)                                                                                   gaccgaccTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCACCGAGTCTGGTGTTTATCGCCGTGGATaa  <  1:150339/90‑1 (MQ=255)                                                                                       |                                                                                      TGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCACCGAGTCTGGTGTTTATCGCCGTGGATAA  >  NZ_CP009273/2013782‑2013953

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑