Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,018,798	C→A	intergenic (+38/‑57)	rmuC → / → ubiE	putative recombination limiting protein RmuC/bifunctional 2‑octaprenyl‑6‑methoxy‑1,4‑benzoquinone methylase and S‑adenosylmethionine:2‑DMK methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,018,798	0	C	A	100.0%	154.0 / NA	44	intergenic (+38/‑57)	rmuC/ubiE	putative recombination limiting protein RmuC/bifunctional 2‑octaprenyl‑6‑methoxy‑1,4‑benzoquinone methylase and S‑adenosylmethionine:2‑DMK methyltransferase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (26/18);  total (26/18)

CAGGATGAAGAGTATCGACTTCGGTCGGTTCCGGAGCAGCCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGCATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACAAAAAGCGGATATGGTCGCC  >  NC_000913/4018668‑4018932                                                                                                                                   |                                                                                                                                       cAGGATGAAGAGTATCGACTTCGGTCGGTTCCGGAGCAGCCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGcc                                                                                                                               <  1:293267/140‑1 (MQ=255)   ggATGAAGAGTATCGACTTCGGTCGGTTCCGGAGCAGCCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCa                                                                                                                             <  1:56573/140‑1 (MQ=255)     aTGAAGGGTATCGACTTCGGTCGGTTCCGGAGCAGCCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGGGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAAt                                                                                                                           <  2:714210/140‑1 (MQ=255)     aTGAAGAGTATCGACTTCGGTCGGTTCCGGAGCAGCCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAAt                                                                                                                           <  2:371723/140‑1 (MQ=255)     aTGAAGAGTATCGACTTCGGTCGGTTCCGGAGCAGCCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAAt                                                                                                                           >  2:549497/1‑140 (MQ=255)             tATCGACTTCGGTCGGTTCCGGAGCAGCCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTaca                                                                                                                   >  2:487308/1‑140 (MQ=255)              aTCGACTTCGGTCGGTTCCGGAGCAGCCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTacac                                                                                                                  >  2:489500/1‑140 (MQ=255)              aTCGACTTCGGTCGGTTCCGGAGCAGCCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTacac                                                                                                                  >  2:634113/1‑140 (MQ=255)                                     cagcCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAg                                                                                           >  2:33/1‑140 (MQ=255)                                      agcCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGc                                                                                          <  2:34427/140‑1 (MQ=255)                                      agcCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGc                                                                                          <  1:489500/140‑1 (MQ=255)                                       gcCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCa                                                                                         >  1:461517/1‑140 (MQ=255)                                                 gaAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTgaga                                                                               <  2:574829/140‑1 (MQ=255)                                                   aGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGAtg                                                                             <  2:245273/140‑1 (MQ=255)                                                     cTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGAtggt                                                                           >  2:271736/1‑140 (MQ=255)                                                        aTCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGa                                                                        <  2:2090/140‑1 (MQ=255)                                                            aCGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAg                                                                    >  2:731519/1‑140 (MQ=255)                                                              gcgATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTc                                                                  >  1:337514/1‑140 (MQ=255)                                                              gcgATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTc                                                                  >  1:227576/1‑140 (MQ=255)                                                                     tgaATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGaa                                                           >  1:21254/1‑140 (MQ=255)                                                                           taATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGACGGTGGATAAGTCACAAGAAacgacg                                                     <  2:545127/140‑1 (MQ=255)                                                                              tCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCAc                                                  >  1:391076/1‑140 (MQ=255)                                                                                 gcagTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGTATAAGTCACAAGAAACGACGCACttt                                               <  2:604379/140‑1 (MQ=255)                                                                                  cagTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTg                                              <  2:218715/140‑1 (MQ=255)                                                                                  cagTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTg                                              >  2:436791/1‑140 (MQ=255)                                                                                   agTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTgg                                             >  2:410748/1‑140 (MQ=255)                                                                                           tAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGa                                     <  2:440857/140‑1 (MQ=255)                                                                                            aGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGAc                                    <  2:461517/140‑1 (MQ=255)                                                                                                 aTTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTcg                               >  2:173526/1‑140 (MQ=255)                                                                                                   tGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTcgcg                             <  2:338818/140‑1 (MQ=255)                                                                                                     ggAGTAGTTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGaa                           <  1:33/140‑1 (MQ=255)                                                                                                       agtagtTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAgg                         >  2:396093/1‑140 (MQ=255)                                                                                                           gtTAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACa                     >  2:224271/1‑140 (MQ=255)                                                                                                            ttAAGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACaa                    >  2:6487/1‑140 (MQ=255)                                                                                                               aGCCGGGTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACaaaaa                 <  2:227576/140‑1 (MQ=255)                                                                                                                   gggTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACAAAAAGCgg             <  1:731519/140‑1 (MQ=255)                                                                                                                   gggTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACAAAAAGCgg             >  2:701027/1‑140 (MQ=255)                                                                                                                    ggTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACAAAAAGCGGa            >  2:480848/1‑140 (MQ=255)                                                                                                                    ggTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACAAAAAGCGGa            >  1:280591/1‑140 (MQ=255)                                                                                                                    ggTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACAAAAAGCGGa            >  1:44688/1‑140 (MQ=255)                                                                                                                    ggTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACAAAAAGCGGa            >  2:227711/1‑140 (MQ=255)                                                                                                                     gTAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACAAAAAGCGGat           >  2:439409/1‑140 (MQ=255)                                                                                                                      tAGAAATCTAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACAAAAAGCGGata          >  1:188431/1‑140 (MQ=255)                                                                                                                              tAGGGAATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACAAAAAGCGGATATGGTCGcc  >  1:279820/1‑140 (MQ=255)                                                                                                                                   |                                                                                                                                       CAGGATGAAGAGTATCGACTTCGGTCGGTTCCGGAGCAGCCGAATGATGAAGCTTATCAACGCGATGATGAATATAATCAGCAGTCGCGCTAGCCCATTGGGAGTAGTTAAGCCGGGTAGAAATCTAGGGCATCGACGCCCAATCTGTTACACTTCTGGAACAATTTTTTGATGAGCAGGCATTGAGATGGTGGATAAGTCACAAGAAACGACGCACTTTGGTTTTCAGACCGTCGCGAAGGAACAAAAAGCGGATATGGTCGCC  >  NC_000913/4018668‑4018932

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑