Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,849,792	(C)5→4	coding (345/1503 nt)	uhpB ←	sensory histidine kinase in two‑component regulatory sytem with UhpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,849,788	0	C	.	100.0%	161.4 / NA	40	coding (349/1503 nt)	uhpB	sensory histidine kinase in two‑component regulatory sytem with UhpA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (19/21);  total (19/21)

CGAGATAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCGCCCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGC  >  NC_000913/3849650‑3849908                                                                                                                                           |                                                                                                                         cGAGATAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAAcgccgc                                                                                                                          <  2:1327197/139‑1 (MQ=255)  gagaTAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACgccgcc                                                                                                                         >  2:1074300/1‑139 (MQ=255)              gAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCa                                                                                                            >  2:837909/1‑139 (MQ=255)              gAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCa                                                                                                            >  2:1441267/1‑139 (MQ=255)               aaCACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCaa                                                                                                           >  2:1004147/1‑139 (MQ=255)                   ccAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTg                                                                                                       <  1:1074300/139‑1 (MQ=255)                           atCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTc                                                                                               >  1:1159922/1‑139 (MQ=255)                                 gCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTg                                                                                         >  2:1438587/1‑139 (MQ=255)                                 gCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTg                                                                                         >  1:1200031/1‑139 (MQ=255)                                 gCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTg                                                                                         >  1:1193908/1‑139 (MQ=255)                                      cGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGc                                                                                    >  2:46842/1‑139 (MQ=255)                                      cGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGc                                                                                    >  2:1422227/1‑139 (MQ=255)                                         cAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGAt                                                                                 <  1:711568/139‑1 (MQ=255)                                                     tAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCa                                                                     <  1:1004147/139‑1 (MQ=255)                                                     tAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCa                                                                     <  2:1193908/139‑1 (MQ=255)                                                     tAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCa                                                                     <  2:1200031/139‑1 (MQ=255)                                                                   gcgcATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGt                                                       <  1:1438587/139‑1 (MQ=255)                                                                            aCGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGt                                              <  1:1422227/139‑1 (MQ=255)                                                                            aCGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGt                                              <  1:837909/139‑1 (MQ=255)                                                                                ctctTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             <  1:1273957/136‑1 (MQ=255)                                                                                ctctTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             >  2:1273957/1‑136 (MQ=255)                                                                                   tttGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAAcgccgc                                                                                                                          >  2:139551/1‑57 (MQ=255)                                                                                   tttGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAAcgccgc                                                                                                                          <  1:139551/57‑1 (MQ=255)                                                                                   tttGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACg                                                                                            >  2:227597/1‑86 (MQ=255)                                                                                   tttGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACg                                                                                            <  1:227597/86‑1 (MQ=255)                                                                                   tttGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTAc                                       >  2:229728/1‑139 (MQ=255)                                                                                      gCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGa                                    <  1:1441267/139‑1 (MQ=255)                                                                                          tGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             >  2:700297/1‑126 (MQ=255)                                                                                          tGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             <  1:700297/126‑1 (MQ=255)                                                                                          tGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGatcat                                >  1:875281/1‑139 (MQ=255)                                                                                           gCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGAt                                                                                 >  1:98436/1‑89 (MQ=255)                                                                                           gCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGAt                                                                                 <  2:98436/89‑1 (MQ=255)                                                                                           gCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             <  1:767823/125‑1 (MQ=255)                                                                                           gCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             >  2:767823/1‑125 (MQ=255)                                                                                                      ggCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGatcat                                >  2:1420479/1‑127 (MQ=255)                                                                                                      ggCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGatcat                                <  1:1420479/127‑1 (MQ=255)                                                                                                      ggCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGaaa                    <  2:875281/139‑1 (MQ=255)                                                                                                           cGACTGCAACAACGCCGCCGCCGTTAACGCCGcccc                                                                                                                       >  1:513185/1‑36 (MQ=255)                                                                                                           cGACTGCAACAACGCCGCCGCCGTTAACGCCGcccc                                                                                                                       <  2:513185/36‑1 (MQ=255)                                                                                                            gACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGAt                                                                       >  2:1280789/1‑82 (MQ=255)                                                                                                            gACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGAt                                                                       <  1:1280789/82‑1 (MQ=255)                                                                                                            gACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGt              <  1:654862/139‑1 (MQ=255)                                                                                                              cTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTa            <  2:1159922/139‑1 (MQ=255)                                                                                                                        gccgccgccGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGc  <  1:229728/139‑1 (MQ=255)                                                                                                                            ccgccgTTAACGCCG‑CCCCTGTAACAGCAAGGTgcgc                                                                                                    <  1:844081/37‑1 (MQ=37)                                                                                                                            ccgccgTTAACGCCG‑CCCCTGTAACAGCAAGGTgcgc                                                                                                    >  2:844081/1‑37 (MQ=37)                                                                                                                                           |                                                                                                                         CGAGATAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCGCCCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGC  >  NC_000913/3849650‑3849908

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑