Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,244,726	A→G	intergenic (‑199/‑2)	ycgR ← / → ymgE	flagellar brake protein YcgR/PF04226 family protein YmgE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,244,726	0	A	G	100.0%	201.5 / NA	53	intergenic (‑199/‑2)	ycgR/ymgE	flagellar brake protein YcgR/PF04226 family protein YmgE
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (34/19);  total (34/19)

ATACAAATGCGTGAATATTTTTTACATGTTGTTCTTAAATCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAACATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATTCTCGGGATAGTCGGTGCGGTGGTCGGCGG  >  NC_000913/1244589‑1244858                                                                                                                                          |                                                                                                                                     aTACAAATGCGTGAATATTTTTTACATGTTGTTCTTAAATCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCa                                                                                                                                    >  2:976498/1‑140 (MQ=255)              aaTATTTTTTACATGTTGTTCTTAAATCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGc                                                                                                                       <  2:568043/140‑1 (MQ=255)                    ttttACATGTTGTTCTTAAATCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGat                                                                                                                 <  1:896587/140‑1 (MQ=255)                         cATGTTGTTCTTAAATCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTAttt                                                                                                            >  2:542474/1‑140 (MQ=255)                          aTGTTGTTCTTAAATCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTAtttt                                                                                                           <  1:901663/140‑1 (MQ=255)                           tgttgtTCTTAAATCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTAttttt                                                                                                          >  2:539701/1‑140 (MQ=255)                              tgttCTTAAATCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGAc                                                                                                       >  1:714904/1‑140 (MQ=255)                                  cTTAAATCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGa                                                                                                   >  2:1003854/1‑140 (MQ=255)                                     aaaTCAGCCGACATACGCCCAGCATCGATCCCGTCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAg                                                                                                >  2:72361/1‑140 (MQ=255)                                      aaTCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGc                                                                                               <  1:858644/140‑1 (MQ=255)                                        tCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCg                                                                                             >  2:366248/1‑140 (MQ=255)                                          aGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGc                                                                                           >  1:523251/1‑140 (MQ=255)                                          aGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGc                                                                                           >  2:433235/1‑140 (MQ=255)                                          aGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGCAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGTATTATTGCATGGATTATTTTTGACCTGAAAGCCGGc                                                                                           >  2:711015/1‑140 (MQ=255)                                            ccGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCAt                                                                                         >  2:493765/1‑140 (MQ=255)                                             cGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCAtt                                                                                        <  1:131544/140‑1 (MQ=255)                                                    cGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCa                                                                                 >  1:356500/1‑140 (MQ=255)                                                      cccAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAg                                                                               >  2:567138/1‑140 (MQ=255)                                                      cccAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAg                                                                               <  1:150235/140‑1 (MQ=255)                                                       ccAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGc                                                                              >  2:993273/1‑140 (MQ=255)                                                          gCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTaa                                                                           >  1:871928/1‑140 (MQ=255)                                                          gCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTaa                                                                           >  1:423038/1‑140 (MQ=255)                                                               gATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATg                                                                      >  1:772655/1‑140 (MQ=255)                                                                 tCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGcc                                                                    <  1:366248/140‑1 (MQ=255)                                                                     gCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCgggg                                                                >  1:87541/1‑140 (MQ=255)                                                                     gCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCgggg                                                                >  1:464316/1‑140 (MQ=255)                                                                          tGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGa                                                           <  1:976498/140‑1 (MQ=255)                                                                          tGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGa                                                           <  2:54836/140‑1 (MQ=255)                                                                           gCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGAt                                                          >  1:866126/1‑140 (MQ=255)                                                                               ataCTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGAtggtg                                                      <  2:655852/140‑1 (MQ=255)                                                                                     agagCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGAt                                                >  1:540145/1‑140 (MQ=255)                                                                                     agagCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGAt                                                >  1:19990/1‑140 (MQ=255)                                                                                     agagCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGAt                                                >  1:502890/1‑140 (MQ=255)                                                                                     agagCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGAt                                                <  2:431902/140‑1 (MQ=255)                                                                                     agagCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGAt                                                >  1:872300/1‑140 (MQ=255)                                                                                     agagCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGAt                                                <  1:756172/140‑1 (MQ=255)                                                                                        gCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGAtttt                                             >  1:860463/1‑140 (MQ=255)                                                                                          gTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTc                                           <  1:329987/140‑1 (MQ=255)                                                                                           ttGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTcc                                          >  1:646583/1‑140 (MQ=255)                                                                                           ttGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTcc                                          >  1:788613/1‑140 (MQ=255)                                                                                           ttGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTcc                                          >  1:383745/1‑140 (MQ=255)                                                                                             gATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTg                                        <  2:356500/140‑1 (MQ=255)                                                                                             gATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGAGGATTTTTCCTg                                        >  1:816023/1‑140 (MQ=255)                                                                                                 tAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCt                                    >  2:959940/1‑140 (MQ=255)                                                                                                        ttCTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATtct                             >  2:894862/1‑140 (MQ=255)                                                                                                          cTTGCGTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATTCTCg                           <  1:433235/140‑1 (MQ=255)                                                                                                               gTCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATTCTCGGGATa                      >  1:754171/1‑140 (MQ=255)                                                                                                                tCCGATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATTCTCGGGATAg                     >  2:28688/1‑140 (MQ=255)                                                                                                                   gATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATTCTCGGGATAGTcg                  <  2:464316/140‑1 (MQ=255)                                                                                                                   gATTCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATTCTCGGGATAGTcg                  <  2:87541/140‑1 (MQ=255)                                                                                                                      tCATCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATTCTCGGGATAGTcggtg               <  2:772655/140‑1 (MQ=255)                                                                                                                         tCGAAACGAGGGCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATTCTCGGGATAGTcggtgcgg            <  2:383745/140‑1 (MQ=255)                                                                                                                                  gggCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATTCTCGGGATAGTCGGTGCGGTGGTcggcg   >  2:915258/1‑140 (MQ=255)                                                                                                                                   ggCCTGAGCATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATTCTCGGGATAGTCGGTGCGGTGGTcggcgg  >  1:811285/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                     ATACAAATGCGTGAATATTTTTTACATGTTGTTCTTAAATCAGCCGACATACGCCCAGCATCGATCCCGCCCTTGCCTATACTTAGAGCGTTGATGTAAGCATTTCTTGCGTCCGATTCATCGAAACGAGGGCCTGAACATGGGAATTATTGCCTGGATTATTTTTGACCTGATAGCCGGCATTATCGCCAAGCTAATCATGCCGGGGCGTGATGGTGGTGGATTTTTCCTGACCTGTATTCTCGGGATAGTCGGTGCGGTGGTCGGCGG  >  NC_000913/1244589‑1244858

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: ‑