Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,556,470	G→T	P127Q (CCG→CAG)	rtcA ←	RNA 3'‑terminal phosphate cyclase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,556,470	0	G	T	100.0%	200.2 / NA	57	P127Q (CCG→CAG)	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (25/32);  total (25/32)

TTGCCACCACACCGCCTCCGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACGGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCA  >  NC_000913/3556345‑3556602                                                                                                                              |                                                                                                                                     ttGCCACCACACCGCCTCCGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTgccg                                                                                                                        <  2:1208252/140‑1 (MQ=255) ttGCCACCACACCGCCTCCGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTgccg                                                                                                                        <  2:2104394/140‑1 (MQ=255)    ccaccaCACCGCCTCCGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGccgccg                                                                                                                     <  1:1225392/140‑1 (MQ=255)    ccaccaCACCGCCTCCGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGccgccg                                                                                                                     <  2:780204/140‑1 (MQ=255)      accacACCGCCTCCGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCt                                                                                                                   <  2:259337/140‑1 (MQ=255)          cacCGCCTCCGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACt                                                                                                               <  2:1459165/140‑1 (MQ=255)             cGCCTCCGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCa                                                                                                            >  1:1011849/1‑140 (MQ=255)              gCCTCCGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCaa                                                                                                           >  1:106911/1‑140 (MQ=255)              gCCTCCGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCACCGACTGGTTATCGGTGCCGCCGCTCACTTCaa                                                                                                           <  2:1731781/140‑1 (MQ=255)                  ccGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACAcg                                                                                                       >  1:1826462/1‑140 (MQ=255)                      cAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGaa                                                                                                   <  1:1410132/140‑1 (MQ=255)                         ggTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGt                                                                                                >  1:1929560/1‑140 (MQ=255)                         ggTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGt                                                                                                >  1:333309/1‑140 (MQ=255)                           tAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTcc                                                                                              <  1:678196/140‑1 (MQ=255)                                   gTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCaa                                                                                      >  2:16004/1‑140 (MQ=255)                                     ggCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAAc                                                                                    >  2:514987/1‑140 (MQ=255)                                               cGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTTACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCgg                                                                          >  2:1425716/1‑140 (MQ=255)                                               cGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCgg                                                                          >  1:2053068/1‑140 (MQ=255)                                               cGTGGTTTGCTGATGAATTCCTAATTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCgg                                                                          >  1:2011131/1‑140 (MQ=255)                                                gTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCggg                                                                         <  1:1947647/140‑1 (MQ=255)                                                gTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAACCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCggg                                                                         <  1:1461914/140‑1 (MQ=255)                                                 tGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGgc                                                                        >  1:923842/1‑140 (MQ=255)                                                  ggTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGgca                                                                       <  2:406667/140‑1 (MQ=255)                                                        cTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCg                                                                 <  2:992576/140‑1 (MQ=255)                                                          gatgaATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGtt                                                               <  2:964456/140‑1 (MQ=255)                                                           atgaATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGttt                                                              >  2:1963204/1‑140 (MQ=255)                                                              aaTTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTgca                                                           >  2:1584016/1‑140 (MQ=255)                                                              aaTTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTgca                                                           >  1:299964/1‑140 (MQ=255)                                                                  ccTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCAc                                                       <  1:677027/140‑1 (MQ=255)                                                                  ccTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGATATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCAc                                                       <  2:1299185/140‑1 (MQ=255)                                                                   cTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCAcc                                                      <  1:1220129/140‑1 (MQ=255)                                                                          cGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTAc                                               >  1:1416436/1‑140 (MQ=255)                                                                                tagcGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTc                                         <  1:61538/139‑1 (MQ=255)                                                                                cagcGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTc                                         >  1:649123/1‑140 (MQ=255)                                                                                cagcGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTc                                         <  2:149591/140‑1 (MQ=255)                                                                                cagcGGCTCCAGCACCAGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTc                                         <  2:415629/140‑1 (MQ=255)                                                                                  gcGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCg                                       <  2:333309/140‑1 (MQ=255)                                                                                         cAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTAc                                <  2:1416436/140‑1 (MQ=255)                                                                                          aGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTAcc                               >  1:1370252/1‑140 (MQ=255)                                                                                          aGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTAcc                               <  2:1621249/140‑1 (MQ=255)                                                                                          aGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTAcc                               >  1:2205094/1‑140 (MQ=255)                                                                                          aGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTAcc                               >  2:575814/1‑140 (MQ=255)                                                                                             aCCCGGCGGATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGAt                            >  2:1931123/1‑140 (MQ=255)                                                                                                cggcggATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGc                         >  1:856298/1‑140 (MQ=255)                                                                                                cggcggATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGc                         >  2:1115854/1‑140 (MQ=255)                                                                                                 ggcggATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCa                        <  2:106911/140‑1 (MQ=255)                                                                                                   cggATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCaaa                      <  1:473518/140‑1 (MQ=255)                                                                                                   cggATAAAATCCGCAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCaaa                      >  2:1242670/1‑140 (MQ=255)                                                                                                             ccGCAGGCGGCGCCGAATGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATcg            <  1:176197/140‑1 (MQ=255)                                                                                                                cAGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATcgccg         >  1:267766/1‑140 (MQ=255)                                                                                                                 aGGCGGCGCCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATcgccgc        >  2:292274/1‑140 (MQ=255)                                                                                                                      gcgcCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCgcgc   <  1:949569/140‑1 (MQ=255)                                                                                                                       cgcCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGGTAGCAAAGCGGTAATCGCCGCCGCGCa  <  1:2150897/140‑1 (MQ=255)                                                                                                                       cgcCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCa  <  1:1951644/140‑1 (MQ=255)                                                                                                                       cgcCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCa  <  2:1004405/140‑1 (MQ=255)                                                                                                                       cgcCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCa  <  2:649123/140‑1 (MQ=255)                                                                                                                       cgcCGACTGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCa  <  1:622752/140‑1 (MQ=255)                                                                                                                              |                                                                                                                                     TTGCCACCACACCGCCTCCGGCAGGGTAAAAACCGTGGCGTAACAGCGTGGTTTGCTGATGAATTCCTATTTTCGCCAGCAGCGGCTCCAGCACCCGGCGGATAAAATCCGCAGGCGGCGCCGACGGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCA  >  NC_000913/3556345‑3556602

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑