Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,053,704	G→A	I825I (ATC→ATT)	torS ←	hybrid sensory histidine kinase in two‑component regulatory system with TorR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,053,704	0	G	A	100.0%	234.0 / NA	68	I825I (ATC→ATT)	torS	hybrid sensory histidine kinase in two‑component regulatory system with TorR
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/38);  total (30/38)

CCCAGACTCGAGCAACTGCTTTTTAGCTGATGCGCGGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGGATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTGCGCCAGTAACTGACCGAGCACTTCACGCGGCACCGGTTTAGGGA  >  NC_000913/1053570‑1053837                                                                                                                                       |                                                                                                                                      cccAGACTCGAGCAACTGCTTTTTAGCTGATGCGCGGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAAtct                                                                                                                                   >  1:1157029/1‑139 (MQ=255)   cAGACTCGAGCAACTGCTTTTTAGCTGATGCGCGGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAAtcttc                                                                                                                                 >  2:807946/1‑139 (MQ=255)     gACTCGAGCAACTGCTTTTTAGCTGATGCGCGGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTtctc                                                                                                                               >  2:364728/1‑139 (MQ=255)       cTCGAGCAACTGCTTTTTAGCTGATGCGCGGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCg                                                                                                                             <  2:1216731/139‑1 (MQ=255)       cTCGAGCAACTGCTTTTTAGCTGATGCGCGGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCg                                                                                                                             <  2:1215350/139‑1 (MQ=255)         cGAGCAACTGCTTTTTAGCTGATGCGCGGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTc                                                                                                                           >  2:1091452/1‑139 (MQ=255)               aCTGCTTTTTAGCTGATGCGCGGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCAtt                                                                                                                     <  1:57319/139‑1 (MQ=255)                 tGCTTTTTAGCTGATGCGCGGCATGCTTTATTTTCTCGCTATCCTGACTGGCGCCGGCAATGTCGATTTCATCGAGAAGCGGCAAGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTaa                                                                                                                   <  2:966051/139‑1 (MQ=255)                           cTGATGCGCGGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCt                                                                                                         <  1:1091452/139‑1 (MQ=255)                           cTGATGCGCGGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCt                                                                                                         >  1:1144394/1‑139 (MQ=255)                                   cgGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAg                                                                                                 <  1:1457112/139‑1 (MQ=255)                                          cTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGAt                                                                                          <  1:833834/139‑1 (MQ=255)                                               ttttCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATc                                                                                     <  1:364728/139‑1 (MQ=255)                                                     cGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTc                                                                                                                           >  2:620098/1‑95 (MQ=255)                                                     cGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTc                                                                                                                           <  1:620098/95‑1 (MQ=255)                                                     cGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGa                                                                               <  1:506807/139‑1 (MQ=255)                                                     cGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATATTCATTGAGTTGCGATACATCCAGCGa                                                                               >  2:489144/1‑139 (MQ=255)                                                       cTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGAtt                                                                             >  1:792085/1‑139 (MQ=255)                                                       cTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGAtt                                                                             <  1:677113/139‑1 (MQ=255)                                                                    cgcgGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGt                                                                                                <  1:147581/107‑1 (MQ=255)                                                                    cgcgGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGt                                                                                                >  2:147581/1‑107 (MQ=255)                                                                      cgGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAAtcttct                                                                                                                                >  1:603356/1‑73 (MQ=255)                                                                      cgGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAAtcttct                                                                                                                                <  2:603356/73‑1 (MQ=255)                                                                      cgGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACtt                                                              <  1:807946/139‑1 (MQ=255)                                                                      cgGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACtt                                                              >  1:903721/1‑139 (MQ=255)                                                                       gggCAATGTCGATTTCATCGATAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTg                                                             <  1:863102/139‑1 (MQ=255)                                                                        ggCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGa                                                                               >  1:1238918/1‑120 (MQ=255)                                                                        ggCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGa                                                                               <  2:1238918/120‑1 (MQ=255)                                                                         gCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCa                                                           <  2:739445/139‑1 (MQ=255)                                                                             tGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATa                                                                                         >  2:389444/1‑105 (MQ=255)                                                                             tGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATa                                                                                         <  1:389444/105‑1 (MQ=255)                                                                             tGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTg                                                       <  2:1144394/139‑1 (MQ=255)                                                                                  aTTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGt                                                         <  2:1425913/132‑1 (MQ=255)                                                                                  aTTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGt                                                         >  1:1425913/1‑132 (MQ=255)                                                                                         cGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTgcgc                                           <  2:1451554/139‑1 (MQ=255)                                                                                         cGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTgcgc                                           <  2:1157029/139‑1 (MQ=255)                                                                                                                gtAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACt                                                               <  1:126524/96‑1 (MQ=255)                                                                                                                gtAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACt                                                               >  2:126524/1‑96 (MQ=255)                                                                                                                 tAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGa                                                                               <  2:1019369/79‑1 (MQ=255)                                                                                                                 tAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGa                                                                               >  1:1019369/1‑79 (MQ=255)                                                                                                                 tAAATAATACCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACCGAGCATCTTCATTGAGTTGCGATa                                                                                         <  2:994708/69‑1 (MQ=255)                                                                                                                 tAAATAATACCAGCCATTCGCGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCCTTGAGTTGCGATa                                                                                         >  1:994708/1‑69 (MQ=255)                                                                                                                    ataataCCAGCCATTCGTGAATCTTCTCCGTCCCCa                                                                                                                       <  2:181032/36‑1 (MQ=255)                                                                                                                    ataataCCAGCCATTCGTGAATCTTCTCCGTCCCCa                                                                                                                       >  1:181032/1‑36 (MQ=255)                                                                                                                      aataCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGc                                                                                                             >  2:832143/1‑44 (MQ=255)                                                                                                                      aataCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGc                                                                                                             <  1:832143/44‑1 (MQ=255)                                                                                                                      aataCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTg                                                             >  2:1071576/1‑92 (MQ=255)                                                                                                                      aataCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTg                                                             >  1:1232321/1‑92 (MQ=255)                                                                                                                      aataCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTg                                                             <  2:1232321/92‑1 (MQ=255)                                                                                                                      aataCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTg                                                             <  1:1071576/92‑1 (MQ=255)                                                                                                                        taCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTGCGCCAGTAACTGACCGAGCACTTCACGCGGCAcc            <  2:347637/139‑1 (MQ=255)                                                                                                                        taCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTGCGCCAGTAACTGACCGAGCACTTCACGCGGCAcc            <  2:903721/139‑1 (MQ=255)                                                                                                                         aCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCAt                                                                                                           <  1:451586/43‑1 (MQ=255)                                                                                                                         aCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCAt                                                                                                           >  2:451586/1‑43 (MQ=255)                                                                                                                         aCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTg                                                                            <  1:1218047/74‑1 (MQ=255)                                                                                                                         aCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTg                                                                            >  2:1218047/1‑74 (MQ=255)                                                                                                                         aCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACt                                                               >  2:1326087/1‑87 (MQ=255)                                                                                                                         aCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACt                                                               <  1:1326087/87‑1 (MQ=255)                                                                                                                         aCCAGCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTGCGCCAGTAACTGACCGAGCACTTCACGCGGCACCg           >  2:1365727/1‑139 (MQ=255)                                                                                                                             gCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTgcgc                                           >  2:1055742/1‑103 (MQ=255)                                                                                                                             gCCATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTgcgc                                           <  1:1055742/103‑1 (MQ=255)                                                                                                                              ccATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCa                                                                                                            >  2:549909/1‑37 (MQ=255)                                                                                                                              ccATTCGTGAATCTTCTCCGTCCCCATTAACTGAGCa                                                                                                            <  1:549909/37‑1 (MQ=255)                                                                                                                                 ttCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATcc                                                                                    >  2:655109/1‑58 (MQ=255)                                                                                                                                 ttCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATcc                                                                                    <  1:655109/58‑1 (MQ=255)                                                                                                                                  tCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTGCGCCAGTAACTGACCGAGCACTTCACGCGGCAcc            <  2:203712/129‑1 (MQ=255)                                                                                                                                  tCGTGAATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTGCGCCAGTAACTGACCGAGCACTTCACGCGGCACCGGTTTAGGGa  >  2:375622/1‑139 (MQ=255)                                                                                                                                  tCGTGAATCTTCTCCGCCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTGCGCCAGTAACTGACCGAGCACTTCACGCGGCAcc            >  1:203712/1‑129 (MQ=255)                                                                                                                                       |                                                                                                                                      CCCAGACTCGAGCAACTGCTTTTTAGCTGATGCGCGGCACGCTTTATTTTCTCGCTATCCTGACTGGCGCGGGCAATGTCGATTTCATCGAGAAGCGGCAGGGCATGTTGTGTAAATAATACCAGCCATTCGTGGATCTTCTCCGTCCCCATTAACTGAGCATCTTCATTGAGTTGCGATACATCCAGCGATTGATCATTATTGACTTGCAGTTGGAGATAGTGCGCCAGTAACTGACCGAGCACTTCACGCGGCACCGGTTTAGGGA  >  NC_000913/1053570‑1053837

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: ‑