Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,020,349	Δ1 bp	coding (263/1005 nt)	fliM →	flagellar motor switch protein FliM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,020,348	0	C	.	100.0%	102.5 / NA	25	coding (262/1005 nt)	fliM	flagellar motor switch protein FliM
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (12/13);  total (12/13)

GCCCGCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCAC  >  NC_000913/2020270‑2020424                                                                               |                                                                             gCCCGCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGcg                                                                             >  2:359362/1‑79 (MQ=255) gCCCGCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGcg                                                                             <  2:359322/80‑2 (MQ=255)    cGCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTAcc                                                                        <  1:359323/81‑1 (MQ=255)           ttCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAAtt                                                                 >  2:359359/1‑81 (MQ=255)           ttCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAAt                                                                  <  1:359324/80‑1 (MQ=255)               tATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGcc                                                             >  2:359367/1‑81 (MQ=255)                   gggCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGc                                                          >  1:359360/1‑80 (MQ=255)                     gCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAAc                                                       <  2:359325/81‑1 (MQ=255)                         ttCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGc                                                   <  2:359326/81‑1 (MQ=255)                            aaCCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCg                                                 <  1:359327/80‑1 (MQ=255)                             aCCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGt                                               >  1:359374/1‑81 (MQ=255)                                  ctgcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGcc                                            <  1:359329/79‑1 (MQ=255)                                  ctgcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCg                                           <  2:359328/80‑1 (MQ=255)                                    gcGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGAc                                         >  2:359368/1‑80 (MQ=255)                                      gtcgtAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCaa                                      >  1:359361/1‑81 (MQ=255)                                          tAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTg                                  <  2:359330/81‑1 (MQ=255)                                                 gATATAACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTa                           <  1:359331/81‑1 (MQ=255)                                                     taACCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATcc                        <  1:359332/80‑1 (MQ=255)                                                       aCCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATc                     >  2:359375/1‑81 (MQ=255)                                                       aCCGTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATc                     >  2:359357/1‑81 (MQ=255)                                                          gTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTg                   >  1:359372/1‑80 (MQ=255)                                                          gTCGGGGCCATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTg                   >  1:359378/1‑80 (MQ=255)                                                                  cATCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTGAAACCGCTg          >  2:359376/1‑81 (MQ=255)                                                                   aTCCGCATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTGAAACCGCTgc         <  1:359333/81‑1 (MQ=255)                                                                        cATTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTGAAACCGCTGCGCGGc    <  2:359334/81‑1 (MQ=255)                                                                         aTTCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCa   >  2:359370/1‑81 (MQ=255)                                                                          ttCAG‑CGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCAc  <  2:359335/81‑1 (MQ=255)                                                                               |                                                                             GCCCGCCATTTTCGTATGGGGCTGTTCAACCTGCTGCGTCGTAGCCCGGATATAACCGTCGGGGCCATCCGCATTCAGCCGTACCATGAATTTGCCCGCAACCTGCCGGTGCCGACCAACCTGAACCTTATCCATCTGAAACCGCTGCGCGGCAC  >  NC_000913/2020270‑2020424

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑