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%	206.7 / NA	64	*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 (26/38);  total (26/38)

AAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGATTCCG  >  NC_000913/4637994‑4638246                                                                                                                               |                                                                                                                               aaGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttctt                                                                                                                    <  1:1708666/139‑1 (MQ=255)       cGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCcaca                                                                                                              <  2:1579166/139‑1 (MQ=255)       cGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCcaca                                                                                                              <  2:11039/139‑1 (MQ=255)          tCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAg                                                                                                           <  1:1465826/139‑1 (MQ=255)             ggggTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCt                                                                                                        <  2:1437999/139‑1 (MQ=255)                    gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCaaa                                                                                                                         >  2:790392/1‑115 (MQ=255)                    gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCaaa                                                                                                                         <  1:790392/115‑1 (MQ=255)                    gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttc                                                                                                                      >  1:1321998/1‑118 (MQ=255)                    gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttc                                                                                                                      <  2:1321998/118‑1 (MQ=255)                    gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTa                                                                                                   >  1:283196/1‑137 (MQ=255)                    gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTa                                                                                                   <  2:283196/137‑1 (MQ=255)                    gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATc                                                                                                 >  1:1448239/1‑139 (MQ=255)                    gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATc                                                                                                 >  1:952594/1‑139 (MQ=255)                    gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATc                                                                                                 >  1:761565/1‑139 (MQ=255)                    gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCACAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACAt                                                                                                             >  1:1651460/1‑127 (MQ=255)                    gCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCACAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACAt                                                                                                             <  2:1651460/127‑1 (MQ=255)                             aGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGt                                                                                                    >  2:635313/1‑127 (MQ=255)                             aGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGt                                                                                                    <  1:635313/127‑1 (MQ=255)                                  ggTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCa                                                                                   <  1:817825/139‑1 (MQ=255)                                   gTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCAt                                                                                       >  2:614075/1‑134 (MQ=255)                                   gTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCAt                                                                                       <  1:614075/134‑1 (MQ=255)                                    tCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCaaa                                                                                 >  1:1635038/1‑139 (MQ=255)                                      gCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttctt                                                                                                                    <  1:408681/102‑1 (MQ=255)                                      gCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttctt                                                                                                                    >  2:408681/1‑102 (MQ=255)                                      gCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAt                                                                                                                        >  2:1261056/1‑98 (MQ=255)                                      gCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAt                                                                                                                        <  1:1261056/98‑1 (MQ=255)                                      gCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAgg                                                                               >  1:421121/1‑139 (MQ=255)                                      gCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAgg                                                                               >  2:1349336/1‑139 (MQ=255)                                       cccGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGga                                                                              <  1:77850/139‑1 (MQ=255)                                         cGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGgaga                                                                            <  1:782768/139‑1 (MQ=255)                                            ttttttAACGCCGAGGCAACGCGGCGAAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTCCACCGTCACTTCACATACCTTCAAATTCTCCCCACATAGTCTTCGTACCCTGCTGCAATTGCAAagaagaaga                                                                         <  2:1148864/136‑1 (MQ=255)                                            ttgtttAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaaga                                                                         <  2:421121/139‑1 (MQ=255)                                            ttgtttAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaaga                                                                         <  1:377836/139‑1 (MQ=255)                                            ttgtttAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaaga                                                                         <  2:1122891/139‑1 (MQ=255)                                                   aCGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGtt                                                                  <  1:1349336/139‑1 (MQ=255)                                                     ggCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTg                                                                                     <  1:1184620/118‑1 (MQ=255)                                                     ggCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTg                                                                                     >  2:1184620/1‑118 (MQ=255)                                                         aaGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATc                                                            >  2:974839/1‑139 (MQ=255)                                                           gTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATccc                                                          <  1:974839/139‑1 (MQ=255)                                                             cACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATccccc                                                        <  2:952594/139‑1 (MQ=255)                                                                      cAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATccccc                                                        >  2:705614/1‑130 (MQ=255)                                                                      cAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATccccc                                                        <  1:705614/130‑1 (MQ=255)                                                                        aCGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGaa                                             <  2:1448239/139‑1 (MQ=255)                                                                        aCGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGaa                                             <  1:972981/139‑1 (MQ=255)                                                                             cAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGa                                        <  1:1668168/139‑1 (MQ=255)                                                                              aGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttctt                                                                                                                    >  2:1544222/1‑62 (MQ=255)                                                                              aGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAAttctt                                                                                                                    <  1:1544222/62‑1 (MQ=255)                                                                                  aGGTNGNGTGCTGGNCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGc                                   <  2:1382085/139‑1 (MQ=255)                                                                                   ggTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaaga                                                                         <  2:1456412/100‑1 (MQ=255)                                                                                   ggTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaaga                                                                         >  1:1456412/1‑100 (MQ=255)                                                                                          tGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTgg                           <  2:1635038/139‑1 (MQ=255)                                                                                          tGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTgg                           >  2:782861/1‑139 (MQ=255)                                                                                            cTGGCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTg                         <  2:761565/139‑1 (MQ=255)                                                                                              ggCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaaga                                                                         <  1:586995/89‑1 (MQ=255)                                                                                              ggCCTCGCTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaaga                                                                         >  2:586995/1‑89 (MQ=255)                                                                                                     cTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGga                                                                              <  1:7739/77‑1 (MQ=255)                                                                                                     cTTCGACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGga                                                                              >  2:7739/1‑77 (MQ=255)                                                                                                         gACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGga                                                                              <  1:637158/73‑1 (MQ=255)                                                                                                         gACTTCACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGga                                                                              >  2:637158/1‑73 (MQ=255)                                                                                                              cACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATccccc                                                        <  2:1316818/90‑1 (MQ=255)                                                                                                              cACCGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATccccc                                                        >  1:1316818/1‑90 (MQ=255)                                                                                                                ccGTCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGAtt     <  1:782861/139‑1 (MQ=255)                                                                                                                   tCACTTCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGATTCCg  >  2:1469581/1‑139 (MQ=255)                                                                                                                       ttCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaa                                                                           >  2:667476/1‑62 (MQ=255)                                                                                                                       ttCACATAACTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGagaa                                                                           <  1:667476/62‑1 (MQ=255)                                                                                                                               |                                                                                                                               AAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAATTCTTCCCACATAGTCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGATTCCG  >  NC_000913/4637994‑4638246

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑