Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,017,423	A→C	E290D (GAA→GAC)	fliI →	flagellum‑specific ATP synthase FliI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,017,423	0	A	C	100.0%	173.3 / NA	45	E290D (GAA→GAC)	fliI	flagellum‑specific ATP synthase FliI
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (28/17);  total (28/17)

TGCGAATGCAGGGTGCCGCCTATGCCACGCGCATTGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGAACCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTTATACCGTGCTCACTGAAGGCGATGACCAG  >  NC_000913/2017287‑2017558                                                                                                                                         |                                                                                                                                        tGCGAATGCAGGGTGCCGCCTATGCCACGCGCATTGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGAcccc                                                                                                                                      <  1:1249960/140‑1 (MQ=255)   cGAATGCAGGGTGCCGCCTATGCCACGCGCATTGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGAcccccc                                                                                                                                    >  2:1271249/1‑140 (MQ=255)     aaTGCAGGGTGCCGCCTATGCCACGCGCATTGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCg                                                                                                                                  <  2:533105/140‑1 (MQ=255)     aaTGCAGGGTGCCGCCTATGCCACGCGCATTGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCg                                                                                                                                  <  2:787047/140‑1 (MQ=255)        gCAGGGTGCCGCCTATGCCACGCGCATTGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTCGCGACCCCCCCGcca                                                                                                                               >  1:455967/1‑140 (MQ=255)          ggggTGCCGCCTATGCCACGCGCATTGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTCGCGACCCCCCCGccacc                                                                                                                             <  2:455967/139‑1 (MQ=255)                    cTATGCCACGCGCATTGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATc                                                                                                                   <  1:141397/140‑1 (MQ=255)                            cgcgCATTGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCg                                                                                                           >  2:605758/1‑140 (MQ=255)                             gcgcATTGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCgg                                                                                                          >  1:440951/1‑140 (MQ=255)                                   tGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTg                                                                                                    >  1:381745/1‑140 (MQ=255)                                               tCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCgg                                                                                        <  2:440951/140‑1 (MQ=255)                                                     tCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTgg                                                                                  >  1:380199/1‑140 (MQ=255)                                                         ggTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGa                                                                              <  2:381745/140‑1 (MQ=255)                                                         ggTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGa                                                                              <  1:1271249/140‑1 (MQ=255)                                                               cATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGc                                                                        >  1:576162/1‑140 (MQ=255)                                                               cATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGc                                                                        >  1:210918/1‑140 (MQ=255)                                                               cATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGc                                                                        <  2:14144/140‑1 (MQ=255)                                                                 tgtgTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCg                                                                      >  2:479016/1‑140 (MQ=255)                                                                    gtTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGaa                                                                   >  1:758748/1‑140 (MQ=255)                                                                    gtTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGaa                                                                   >  1:949305/1‑140 (MQ=255)                                                                         tGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGc                                                              >  2:1074252/1‑140 (MQ=255)                                                                             tATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTa                                                          >  1:827755/1‑140 (MQ=255)                                                                                     cccTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAgcggcggc                                                  >  1:1289143/1‑140 (MQ=255)                                                                                      ccTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAgcggcggcg                                                 >  2:608210/1‑140 (MQ=255)                                                                                      ccTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAgcggcggcg                                                 >  1:296820/1‑140 (MQ=255)                                                                                      ccTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAgcggcggcg                                                 >  1:263106/1‑140 (MQ=255)                                                                                           cccGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCg                                            >  2:778211/1‑140 (MQ=255)                                                                                                tACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTAc                                       >  2:972560/1‑140 (MQ=255)                                                                                                 aCGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTAcc                                      <  2:380199/140‑1 (MQ=255)                                                                                                 aCGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTAcc                                      <  2:949305/140‑1 (MQ=255)                                                                                                 aCGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTAcc                                      <  2:493557/140‑1 (MQ=255)                                                                                                  cgcgATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACcg                                     >  2:877669/1‑140 (MQ=255)                                                                                                   gcgATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACcgc                                    <  2:296820/140‑1 (MQ=255)                                                                                                    cgATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACcgcg                                   >  2:671079/1‑140 (MQ=255)                                                                                                      aTGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGtt                                 >  2:343981/1‑140 (MQ=255)                                                                                                      aTGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGtt                                 <  2:210918/140‑1 (MQ=255)                                                                                                          cccAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTAACCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTtat                             >  2:686466/1‑140 (MQ=255)                                                                                                          cccAGCGTGAAATTGCGCTGCCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGGTTtat                             >  1:26870/1‑140 (MQ=255)                                                                                                           ccAGCGTGAAATTGCGCTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTtata                            <  2:1289143/140‑1 (MQ=255)                                                                                                                         cgcTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGTTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTTATACCGTGCTCACTGaa              >  2:1164504/1‑140 (MQ=255)                                                                                                                           cTGGCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTTATACCGTGCTCACTGAAgg            >  2:728863/1‑140 (MQ=255)                                                                                                                              gCGATTGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTTATACCGTGCTCACTGAAGGCGa         >  1:893862/1‑140 (MQ=255)                                                                                                                                 tttGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTTATACCGTGCTCACTGAAGGCGATGa      <  2:26870/139‑1 (MQ=255)                                                                                                                                   tGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTTATACCGTGCTCACTGAAGGCg          <  2:486415/134‑1 (MQ=255)                                                                                                                                   tGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTTATACCGTGCTCACTGAAGGCg          >  1:486415/1‑134 (MQ=255)                                                                                                                                   tGGCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTTATACCGTGCTCACTGAAGGCGATGAcc    >  1:1064393/1‑140 (MQ=255)                                                                                                                                     gCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTTATACCGTGCTCACTGAAGGCGATGACcag  <  1:343981/140‑1 (MQ=255)                                                                                                                                     gCGACCCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTTATACCGTGCTCACTGAAGGCGATGACcag  <  1:877669/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                        TGCGAATGCAGGGTGCCGCCTATGCCACGCGCATTGCCGAAGATTTTCGCGATCGTGGTCAGCATGTGTTGCTGATTATGGACTCCCTCACCCGCTACGCGATGGCCCAGCGTGAAATTGCGCTGGCGATTGGCGAACCCCCCGCCACCAAAGGTTATCCACCGTCGGTGTTTGCCAAATTACCGGCACTGGTCGAGCGTGCCGGAAATGGCATTAGCGGCGGCGGCTCGATTACCGCGTTTTATACCGTGCTCACTGAAGGCGATGACCAG  >  NC_000913/2017287‑2017558

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑