Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,788,278	G→A	*278* (TAG→TAA)	ppsR →	PEP synthase kinase and PEP synthase pyrophosphorylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,788,278	0	G	A	100.0%	188.0 / NA	59	*278* (TAG→TAA)	ppsR	PEP synthase kinase and PEP synthase pyrophosphorylase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (33/26);  total (33/26)

GGATGGAAGTCGCGGAAGTGGAAGCCTTGTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAGAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATCGTGATGCGCATCACTTCCCGGCAGTCCTGCCGT  >  NC_000913/1788145‑1788407                                                                                                                                      |                                                                                                                                  ggATGGAAGTCGCGGAAGTGGAAGCCTTGTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAAc                                                                                                                              <  2:768604/139‑1 (MQ=255)  gATGGAAGTCGCGGAAGTGGAAGCCTTGTACCGTAATAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACt                                                                                                                             <  1:663678/139‑1 (MQ=255)        aGTCGCGGAAGTTGAAGCCTTGTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCa                                                                                                                       <  2:579231/139‑1 (MQ=255)           cgcgGAAGTGGAAGCCTTGTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTa                                                                                                                    >  2:506496/1‑139 (MQ=255)            gcgGAAGTGGAAGCCTTGTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAg                                                                                                                   >  1:818749/1‑139 (MQ=255)            gcgGAAGTGGAAGCCTTGTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAg                                                                                                                   >  1:849349/1‑139 (MQ=255)                 aGTGGAAGCCTTGTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTAt                                                                                                              >  2:447556/1‑139 (MQ=255)                          cTTGTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGtt                                                                                                     >  2:573533/1‑139 (MQ=255)                          cTTGTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGtt                                                                                                     <  1:172888/139‑1 (MQ=255)                           ttGTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTa                                                                                                    <  2:398778/139‑1 (MQ=255)                             gTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATc                                                                                                  >  2:702400/1‑139 (MQ=255)                                   tAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTa                                                                                            <  1:447556/139‑1 (MQ=255)                                   tAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTa                                                                                            >  1:1035952/1‑139 (MQ=255)                                    aaaaaTCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTaa                                                                                           >  1:605040/1‑139 (MQ=255)                                                ccGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAg                                                                               <  2:849349/139‑1 (MQ=255)                                                      aTTAACATTACCAATTATTCGGTAGAAGAGATTGCCATCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAAGTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCATCCGGCGCGGTGTGa                                                                         <  1:269715/139‑1 (MQ=255)                                                       ttAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGac                                                                        <  1:551631/139‑1 (MQ=255)                                                             gTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCt                                                                  <  1:925032/139‑1 (MQ=255)                                                               aCCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCg                                                                >  1:30577/1‑139 (MQ=255)                                                                ccAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGATACACCTCGc                                                               >  2:623295/1‑139 (MQ=255)                                                                ccAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGc                                                               >  1:110436/1‑139 (MQ=255)                                                                ccAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGc                                                               >  2:342140/1‑139 (MQ=255)                                                                ccAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGc                                                               >  2:791855/1‑139 (MQ=255)                                                                    ttattCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTa                                                                                                    <  1:218353/98‑1 (MQ=255)                                                                    ttattCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTa                                                                                                    >  2:218353/1‑98 (MQ=255)                                                                        tCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCgg                                                                                   <  1:798270/111‑1 (MQ=255)                                                                        tCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCgg                                                                                   >  2:798270/1‑111 (MQ=255)                                                                        tCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGaaa                                                       >  1:401270/1‑139 (MQ=255)                                                                        tCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGaaa                                                       >  2:473819/1‑139 (MQ=255)                                                                        tCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTA‑TTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAAt                                                      >  1:762211/1‑139 (MQ=255)                                                                         cGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAAt                                                      >  1:349851/1‑139 (MQ=255)                                                                         cGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAAt                                                      <  2:30577/139‑1 (MQ=255)                                                                          ggTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATc                                                     >  2:1000885/1‑139 (MQ=255)                                                                          ggTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATc                                                     >  1:131510/1‑139 (MQ=255)                                                                           gTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATca                                                    <  1:573533/139‑1 (MQ=255)                                                                            tAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATcag                                                   >  1:974368/1‑139 (MQ=255)                                                                               aagaGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATcagcag                                                >  2:935733/1‑139 (MQ=255)                                                                                  agaTTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGa                                             <  2:818749/139‑1 (MQ=255)                                                                                      tGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTgg                                         >  1:171230/1‑139 (MQ=255)                                                                                        ccaccaAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGtt                                       <  2:810206/139‑1 (MQ=255)                                                                                          accaAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTa                                     <  2:401270/139‑1 (MQ=255)                                                                                          accaAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTa                                     <  2:605040/139‑1 (MQ=255)                                                                                            caAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATc                                   >  2:799980/1‑139 (MQ=255)                                                                                                    tCGATATCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATCGTGATgcg                           >  1:296680/1‑139 (MQ=255)                                                                                                          tCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCg                                                                                 <  2:125372/79‑1 (MQ=255)                                                                                                          tCATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCg                                                                                 >  1:125372/1‑79 (MQ=255)                                                                                                           cATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGc                                                                                                                  <  1:729503/45‑1 (MQ=255)                                                                                                           cATGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGc                                                                                                                  >  2:729503/1‑45 (MQ=255)                                                                                                            aTGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATCGTGATGCGCATCACtt                   <  1:506496/139‑1 (MQ=255)                                                                                                             tGGGCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATCGTGATGCGCATCACTTc                  >  2:1055166/1‑139 (MQ=255)                                                                                                              gggCCTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATCGTGATGCGCATCACTTcc                 <  2:296680/139‑1 (MQ=255)                                                                                                                gccatagaaaccGAACGTCCTAAAGAACTCTTGCATTAACTTATTTGTCTGTTATCATGCTACACCTCCGGCGAGGTGCGACACACCTCGCACTTGAAATCAGCATCGATTGGTTTATCGTGATGAGCATCACTTCCCg               >  2:688139/11‑139 (MQ=255)                                                                                                                  cTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATcagca                                                 >  1:148683/1‑103 (MQ=255)                                                                                                                  cTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATcagca                                                 <  2:148683/103‑1 (MQ=255)                                                                                                                  cTTAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATCGTGATGCGCATCACTTCCCGGc             >  1:309217/1‑139 (MQ=255)                                                                                                                    tAGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATCGTGATGCGCATCACTTCCCGGCAg           >  1:280245/1‑139 (MQ=255)                                                                                                                     aGTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTA‑TTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATCGTGATGCGCATCACTTCCCGGCAGTc         <  2:762211/139‑1 (MQ=255)                                                                                                                      gTCGCCGAATGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATCGTGATGCGCATCACTTCCCGGCAGTc         <  1:935733/139‑1 (MQ=255)                                                                                                                             aaTGTACTAAAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATCGTGATGCGCATCACTTCCCGGCAGTCCTGCCGt  <  1:473819/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                  GGATGGAAGTCGCGGAAGTGGAAGCCTTGTACCGTAAAAATCAGATCCCGTGGATTAACAGTACCAATTATTCGGTAGAAGAGATTGCCACCAAGATCCTCGATATCATGGGCCTTAGTCGCCGAATGTACTAGAGAACTAGTGCATTAGCTTATTTTTTTGTTATCATGCTAACCACCCGGCGAGGTGTGACACACCTCGCACTTGAAATCAGCAGCGATTGGTTTATCGTGATGCGCATCACTTCCCGGCAGTCCTGCCGT  >  NC_000913/1788145‑1788407

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑