Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,317,409	C→T	G163S (GGC→AGC)	phnL ←	ribophosphonate triphosphate synthase subunit, putative ABC transporter‑related ATPase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,317,409	0	C	T	100.0%	176.3 / NA	55	G163S (GGC→AGC)	phnL	ribophosphonate triphosphate synthase subunit, putative ABC transporter‑related ATPase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (29/26);  total (29/26)

CATGGAAGATGCCTACGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCCGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCACGCGGAACGCCG  >  NC_000913/4317274‑4317542                                                                                                                                        |                                                                                                                                      cATGGAAGATGCCTACGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCtgcg                                                                                                                                    <  1:1224627/139‑1 (MQ=255)     gAAGATGCCTACGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGCTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCg                                                                                                                                >  2:97801/1‑139 (MQ=255)      aaGATGCCTACGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGCTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGa                                                                                                                               <  1:97801/139‑1 (MQ=255)                cGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGAcgcg                                                                                                                     >  1:804318/1‑139 (MQ=255)                 gATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACgcgc                                                                                                                    <  2:56020/139‑1 (MQ=255)                      cTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGctgctg                                                                                                               >  1:128395/1‑139 (MQ=255)                        gcgcCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGtt                                                                                                             <  2:1537321/139‑1 (MQ=255)                         cgcCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTc                                                                                                            >  2:1531703/1‑139 (MQ=255)                           ccACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGc                                                                                                          >  1:1221299/1‑139 (MQ=255)                           ccACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGc                                                                                                          >  1:1484461/1‑139 (MQ=255)                                ggTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCg                                                                                                     <  2:1221299/139‑1 (MQ=255)                                    ttGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCgctgc                                                                                                                 <  1:57012/123‑1 (MQ=255)                                    ttGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCgctgc                                                                                                                 >  2:57012/1‑123 (MQ=255)                                            gcgAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGAt                                                                                         >  1:575020/1‑139 (MQ=255)                                                     ttCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATggtgcc                                                                                   >  1:1008526/1‑136 (MQ=255)                                                     ttCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATggtgcc                                                                                   <  2:1008526/136‑1 (MQ=255)                                                        caccacCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATggtgccaggtgc                                                                             <  2:128395/139‑1 (MQ=255)                                                          ccaccGCGGCGCTGTTTTTGGCGTCCAGCTAGGCGGTAGGTTCGTCAAGCAGCAGAATAGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATggtgcc                                                                                   <  2:1468614/131‑1 (MQ=255)                                                          ccaccGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTTGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATggtgcc                                                                                   >  1:1468614/1‑131 (MQ=255)                                                          ccaccGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATggtg                                                                                     >  2:111967/1‑129 (MQ=255)                                                          ccaccGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATggtg                                                                                     <  1:111967/129‑1 (MQ=255)                                                               gcggcgCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGc                                                                      >  1:111111/1‑139 (MQ=255)                                                               gcggcgCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGc                                                                      >  1:568595/1‑139 (MQ=255)                                                               gcggcgCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGc                                                                      >  1:1301456/1‑139 (MQ=255)                                                                        tttttGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGt                                                                                             <  2:1529427/107‑1 (MQ=255)                                                                        tttttGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGt                                                                                             >  1:1529427/1‑107 (MQ=255)                                                                                gTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAgg                                                     <  2:111111/139‑1 (MQ=255)                                                                                gTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAgg                                                     <  1:907136/139‑1 (MQ=255)                                                                                  ccAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAgg                                                                       <  2:452520/119‑1 (MQ=255)                                                                                  ccAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAgg                                                                       >  1:452520/1‑119 (MQ=255)                                                                                   cAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCgg                                                  >  1:350722/1‑139 (MQ=255)                                                                                              tAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGAcg                                                                                                                       <  1:553454/59‑1 (MQ=255)                                                                                              tAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGAcg                                                                                                                       >  2:553454/1‑59 (MQ=255)                                                                                                    cGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAgg                                                     <  2:441943/119‑1 (MQ=255)                                                                                                    cGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAgg                                                     >  1:441943/1‑119 (MQ=255)                                                                                                     gTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGTGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGt                                                                                             >  1:1457065/1‑78 (MQ=255)                                                                                                     gTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGTGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGt                                                                                             <  2:1457065/78‑1 (MQ=255)                                                                                                        aaGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTa                             <  2:350722/139‑1 (MQ=255)                                                                                                           cagcagAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCg                                                                                                           <  1:208422/58‑1 (MQ=255)                                                                                                           cagcagAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCg                                                                                                           >  2:208422/1‑58 (MQ=255)                                                                                                           cagcagAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGAcgc                                      <  2:316927/127‑1 (MQ=255)                                                                                                           cagcagAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGAcgc                                      >  1:316927/1‑127 (MQ=255)                                                                                                                   tGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGc                  >  1:1190419/1‑139 (MQ=255)                                                                                                                        tAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGgcgc                      <  1:535954/130‑1 (MQ=255)                                                                                                                        tAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGgcgc                      >  2:535954/1‑130 (MQ=255)                                                                                                                           tCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGc                                                                                                          >  1:367380/1‑43 (MQ=255)                                                                                                                           tCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGc                                                                                                          <  2:367380/43‑1 (MQ=255)                                                                                                                           tCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGa                                                                                          <  2:1086708/59‑1 (MQ=255)                                                                                                                           tCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGa                                                                                          >  1:1086708/1‑59 (MQ=255)                                                                                                                           tCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCAcgcg          >  1:817211/1‑139 (MQ=255)                                                                                                                           tCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCAcg            >  2:1710108/1‑137 (MQ=255)                                                                                                                           tCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCAcg            <  1:1710108/137‑1 (MQ=255)                                                                                                                            cgacgaTAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCACGCgg         <  2:749101/139‑1 (MQ=255)                                                                                                                             gacgaTAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCACGCGGa        <  1:644614/139‑1 (MQ=255)                                                                                                                             gacgaTAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAAGTTCGAGGGTGCAAGTTCCCCCAGGCGTTCCGCCACGTTAGGGCGGGGGAGAGAACCGGGGGCTTTAGCGGGGCGGGCTTCAggcgaa        >  1:1448194/1‑137 (MQ=255)                                                                                                                                   aaaGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCACGCGGAACGCCg  <  1:394946/139‑1 (MQ=255)                                                                                                                                        |                                                                                                                                      CATGGAAGATGCCTACGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCCGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCACGCGGAACGCCG  >  NC_000913/4317274‑4317542

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑