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%	30.4 / NA	11	N101D (AAC→GAC)	fliM	flagellar motor switch protein FliM
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (6/5);  total (6/5)

CTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCAC  >  NZ_CP009273/2013784‑2013925                                                                                     |                                                          ctgcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTg                                                      >  2:500438/1‑90 (MQ=255)    cgtcgtAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAAc                                                   <  1:89752/90‑1 (MQ=255)               ggATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCt                                        >  1:155858/1‑90 (MQ=255)                        cGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCt                               >  2:418376/1‑90 (MQ=255)                          tCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGc                                >  1:114836/1‑87 (MQ=255)                          tCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGc                                <  2:114836/87‑1 (MQ=255)                                  aTCCGCTTTCAGCCGTCCCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACt                     <  2:536867/90‑1 (MQ=255)                                  aTCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCgaccgacc                                                        <  1:442187/55‑1 (MQ=255)                                  aTCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCgaccgacc                                                        >  2:442187/1‑55 (MQ=255)                                    ccGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTgg                   >  1:66191/1‑90 (MQ=255)                                       cATTCAGCCGTCCCATGAATTTGCCCGCAACCTGCCGGCGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCt                <  1:552927/90‑1 (MQ=255)                                       cATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCt                <  1:245537/90‑1 (MQ=255)                                                     aTGAATTTGCCCGCAACCTGCCGGTGCCGACCGACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCAc  >  2:5513/1‑90 (MQ=255)                                                                                     |                                                          CTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCACTGGGCTGGTGGTGTTCTCAC  >  NZ_CP009273/2013784‑2013925

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑