Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,638,120	G→A	*475* (TAG→TAA)	creC →	sensory histidine kinase in two‑component regulatory system with CreB or PhoB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,638,120	0	G	A	100.0%	234.3 / NA	73	*475* (TAG→TAA)	creC	sensory histidine kinase in two‑component regulatory system with CreB or PhoB
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (34/39);  total (34/39)

GGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGATTCCG  >  NC_000913/4637986‑4638246                                                                                                                                       |                                                                                                                               gggCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTc                                                                                                                            <  1:1519430/139‑1 (MQ=255)    cAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCaaa                                                                                                                         >  1:577265/1‑139 (MQ=255)         aaGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttctt                                                                                                                    <  1:1087567/139‑1 (MQ=255)         aaGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttctt                                                                                                                    <  1:1291133/139‑1 (MQ=255)            cagcGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACTCTGCGCAACGTGCAGCAAGGGGGCGTGCCGGCATCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTTTTccc                                                                                                                 <  2:1081599/139‑1 (MQ=255)                 gTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCaaa                                                                                                                         >  2:342671/1‑126 (MQ=255)                 gTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCaaa                                                                                                                         <  1:342671/126‑1 (MQ=255)                  tCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAg                                                                                                           <  2:1402658/139‑1 (MQ=255)                            gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATc                                                                                                 >  2:481660/1‑139 (MQ=255)                                     aGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCa                                                                                        <  2:577265/139‑1 (MQ=255)                                       tGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAt                                                                                                                        >  2:255179/1‑105 (MQ=255)                                       tGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAt                                                                                                                        <  1:255179/105‑1 (MQ=255)                                         aGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAt                                                                                                                        >  2:1373615/1‑103 (MQ=255)                                         aGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAt                                                                                                                        <  1:1373615/103‑1 (MQ=255)                                          ggTCGCCCGTTTGTTTAACGGCGACGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCa                                                                                   <  1:858127/139‑1 (MQ=255)                                           gTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCaa                                                                                  >  2:1160454/1‑139 (MQ=255)                                           gTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCaa                                                                                  >  1:408537/1‑139 (MQ=255)                                            tCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCaaa                                                                                 >  1:619487/1‑139 (MQ=255)                                            tCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCa                                                                                   >  1:148961/1‑137 (MQ=255)                                            tCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCa                                                                                   <  2:148961/137‑1 (MQ=255)                                              gCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAgg                                                                               >  2:75600/1‑139 (MQ=255)                                                   tttgtttAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaag                                                                          >  1:186312/1‑139 (MQ=255)                                                    ttgtttAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTTGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaaga                                                                         <  2:619487/139‑1 (MQ=255)                                                    ttgtttAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaaga                                                                         <  2:186312/139‑1 (MQ=255)                                                    ttgtttAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaaga                                                                         <  2:376245/139‑1 (MQ=255)                                                                 aaGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATa                                                                                                            <  1:1179842/91‑1 (MQ=255)                                                                 aaGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATa                                                                                                            >  2:1179842/1‑91 (MQ=255)                                                                 aaGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTg                                                                                     >  1:115430/1‑114 (MQ=255)                                                                 aaGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTg                                                                                     <  2:115430/114‑1 (MQ=255)                                                                        gCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTg                                                     >  1:186835/1‑139 (MQ=255)                                                                           gcgcAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTc                                                  <  1:481660/139‑1 (MQ=255)                                                                            cgcTACGTGCAGGAAGGTGGCGTACTGGCCACGCTTCGACTTCACCGTCACTTCACATAACTTCaaa                                                                                                                         <  1:975883/67‑1 (MQ=255)                                                                            cgcAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCcaca                                                                                                              <  1:772676/78‑1 (MQ=255)                                                                            cgcAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCcaca                                                                                                              >  2:772676/1‑78 (MQ=255)                                                                            cgcAACGTGCAGGAAGGTGGCGTACTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCaaa                                                                                                                         >  2:975883/1‑67 (MQ=255)                                                                                     cAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGa                                        <  1:75600/139‑1 (MQ=255)                                                                                      aGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCa                                                                                   <  1:1407095/95‑1 (MQ=255)                                                                                      aGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCa                                                                                   >  2:1407095/1‑95 (MQ=255)                                                                                            gTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttctt                                                                                                                    >  2:48779/1‑56 (MQ=255)                                                                                            gTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttctt                                                                                                                    <  1:48779/56‑1 (MQ=255)                                                                                             tGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCaa                                                                                                                          <  1:1133103/49‑1 (MQ=255)                                                                                             tGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCaa                                                                                                                          >  2:1133103/1‑49 (MQ=255)                                                                                             tGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCa                                                                                   >  2:1451761/1‑88 (MQ=255)                                                                                             tGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCa                                                                                   <  1:1451761/88‑1 (MQ=255)                                                                                             tGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTg                                <  1:1160454/139‑1 (MQ=255)                                                                                                cGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAt                                                                                                                        <  1:153828/48‑1 (MQ=255)                                                                                                cGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAt                                                                                                                        >  2:153828/1‑48 (MQ=255)                                                                                                  tGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttcttc                                                                                                                   <  2:1402381/51‑1 (MQ=255)                                                                                                  tGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttcttc                                                                                                                   >  1:1402381/1‑51 (MQ=255)                                                                                                  tGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAt                                                                                                                        <  2:494005/46‑1 (MQ=255)                                                                                                  tGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAt                                                                                                                        >  1:494005/1‑46 (MQ=255)                                                                                                  tGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGTTGCCATTGCa                                                                                   <  2:674502/83‑1 (MQ=255)                                                                                                  tGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGTTGCCATTGCa                                                                                   >  1:674502/1‑83 (MQ=255)                                                                                                    cTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACGTAGTCTTCGTATCATGCGGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTCTTCTGGAAAATGACTAGCCTGTTTGGTg                         <  2:408537/139‑1 (MQ=255)                                                                                                     tGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGc                        <  1:1137287/139‑1 (MQ=255)                                                                                                            gCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCcac                                                                                                               >  1:1362515/1‑45 (MQ=255)                                                                                                            gCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCcac                                                                                                               <  2:1362515/45‑1 (MQ=255)                                                                                                             cTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGc                >  2:437127/1‑139 (MQ=255)                                                                                                                   cTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTAT‑CTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATccccc                                                        <  1:1306041/92‑1 (MQ=255)                                                                                                                   cTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTAT‑CTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATccccc                                                        >  2:1306041/1‑92 (MQ=255)                                                                                                                      cACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCtgctgc                                                                                          >  2:479592/1‑56 (MQ=255)                                                                                                                      cACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCtgctgc                                                                                          <  1:479592/56‑1 (MQ=255)                                                                                                                      cACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGtt                              >  2:1090365/1‑116 (MQ=255)                                                                                                                      cACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGtt                              <  1:1090365/116‑1 (MQ=255)                                                                                                                      cACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGa       >  1:1453633/1‑139 (MQ=255)                                                                                                                       aCCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGAt      <  2:1453633/139‑1 (MQ=255)                                                                                                                           tCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGATTCCg  >  1:241922/1‑139 (MQ=255)                                                                                                                             aCTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCa                                                                                   >  2:1312022/1‑56 (MQ=255)                                                                                                                             aCTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCa                                                                                   <  1:1312022/56‑1 (MQ=255)                                                                                                                                tCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTAt                   <  1:104041/117‑1 (MQ=255)                                                                                                                                tCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTAt                   >  2:104041/1‑117 (MQ=255)                                                                                                                                 cacaTAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGtt                              >  2:358826/1‑105 (MQ=255)                                                                                                                                 cacaTAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGtt                              <  1:358826/105‑1 (MQ=255)                                                                                                                                       |                                                                                                                               GGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGATTCCG  >  NC_000913/4637986‑4638246

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: ‑