Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,039,654	(C)5→4	coding (177/1005 nt)	yedY →	membrane‑anchored, periplasmic TMAO, DMSO reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,039,650	0	C	.	100.0%	157.1 / NA	38	coding (173/1005 nt)	yedY	membrane‑anchored, periplasmic TMAO, DMSO reductase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (21/17);  total (21/17)

CCGAGTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCGCCCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCCCGCCGCT  >  NC_000913/2039518‑2039783                                                                                                                                     |                                                                                                                                      ccGAGTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGcccgccccgcc                                                                                                                                 >  2:1418165/1‑136 (MQ=255)    aGTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGa                                                                                                                             >  2:317066/1‑139 (MQ=255)               tttATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGa                                                                                                                  >  2:441539/1‑139 (MQ=255)               tttATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGa                                                                                                                  >  1:744606/1‑139 (MQ=255)                ttATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAg                                                                                                                 <  2:744606/139‑1 (MQ=255)                 tATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGt                                                                                                                >  1:570144/1‑139 (MQ=255)                  aTGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGtt                                                                                                               >  2:689134/1‑139 (MQ=255)                       gCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCa                                                                                                          <  2:460603/139‑1 (MQ=255)                        cGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCaa                                                                                                         >  1:614208/1‑139 (MQ=255)                         gTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAg                                                                                                        >  1:321548/1‑139 (MQ=255)                           cGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGcc                                                                                                      >  1:639192/1‑139 (MQ=255)                                 gtgtTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTgccgc                                                                                                >  2:715127/1‑139 (MQ=255)                                   gtTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCt                                                                                              <  1:317066/139‑1 (MQ=255)                                            aCTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATa                                                                                     >  2:1313719/1‑139 (MQ=255)                                            aCTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATa                                                                                     >  2:1079459/1‑139 (MQ=255)                                            aCTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATa                                                                                     >  1:953319/1‑139 (MQ=255)                                              tGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAAc                                                                                   >  2:237255/1‑139 (MQ=255)                                                          cAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACg                                                                       >  2:496610/1‑139 (MQ=255)                                                            aCTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGcc                                                                     <  1:689134/139‑1 (MQ=255)                                                             cTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCca                                                                    <  1:715127/139‑1 (MQ=255)                                                             cTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCca                                                                    >  2:1148416/1‑139 (MQ=255)                                                             cTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGATGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCAGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCca                                                                    <  1:956584/139‑1 (MQ=255)                                                                   tttctttGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGAt                                                              <  1:441539/139‑1 (MQ=255)                                                                       tttGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATcgcccgcccgc                                                                                                                                       >  1:233390/1‑63 (MQ=255)                                                                       tttGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATcgcccgcccgc                                                                                                                                       <  2:233390/63‑1 (MQ=255)                                                                          gCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGttt                                                       <  2:639192/139‑1 (MQ=255)                                                                              cACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCgg                                                   <  1:1418165/139‑1 (MQ=255)                                                                               aCGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGt                                                  >  2:745482/1‑139 (MQ=255)                                                                                     cgcATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTc                                                      >  2:1454014/1‑129 (MQ=255)                                                                                     cgcATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTc                                                      <  1:1454014/129‑1 (MQ=255)                                                                                     cgcATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTataat                                            <  1:1313719/139‑1 (MQ=255)                                                                                     cgcATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTataat                                            <  1:1259597/139‑1 (MQ=255)                                                                                           ccGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCt                                                                                              <  2:270354/83‑1 (MQ=255)                                                                                           ccGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCt                                                                                              >  1:270354/1‑83 (MQ=255)                                                                                                       gCTGGTTTAAATGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCggg                          <  2:953319/139‑1 (MQ=255)                                                                                                       gCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCggg                          <  2:614208/139‑1 (MQ=255)                                                                                                             ttAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCg                                                    >  2:334864/1‑107 (MQ=255)                                                                                                             ttAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCg                                                    <  1:334864/107‑1 (MQ=255)                                                                                                                  gggAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGc               >  1:1475508/1‑139 (MQ=255)                                                                                                                         aTCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATccc        <  2:1361848/139‑1 (MQ=255)                                                                                                                          tCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCccg       >  2:1165849/1‑139 (MQ=255)                                                                                                                            gcccgcccg‑cccCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCccgcc     >  2:875307/1‑139 (MQ=255)                                                                                                                               cgcccg‑cccCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCCCGCCGCt  >  1:484472/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                      CCGAGTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCGCCCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCCCGCCGCT  >  NC_000913/2039518‑2039783

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑