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%	126.0 / NA	39	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 (22/17);  total (22/17)

GAAGATGCCTACGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCCGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCACGCGGAACGCCG  >  NC_000913/4317278‑4317542                                                                                                                                    |                                                                                                                                      gAAGATGCCTACGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCg                                                                                                                                >  2:1313396/1‑139 (MQ=255)            cGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGAcgcg                                                                                                                     >  1:946218/1‑139 (MQ=255)            cGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGAcgcg                                                                                                                     >  1:906362/1‑139 (MQ=255)            cGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGAcgcg                                                                                                                     >  1:556070/1‑139 (MQ=255)            cGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGAcgcg                                                                                                                     >  1:1266085/1‑139 (MQ=255)             gATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACgcgc                                                                                                                    <  2:946218/139‑1 (MQ=255)                  cTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGctgctg                                                                                                               >  2:1454650/1‑139 (MQ=255)                  cTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGctgctg                                                                                                               >  1:495940/1‑139 (MQ=255)                   tGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCg                                                                                                                                <  1:549326/121‑1 (MQ=255)                   tGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCg                                                                                                                                >  2:549326/1‑121 (MQ=255)                             gTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCgg                                                                                                    <  1:1454650/139‑1 (MQ=255)                                               aGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATggtgcca                                                                                  <  2:457859/139‑1 (MQ=255)                                                         ccGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAg                                                                        >  1:212412/1‑139 (MQ=255)                                                          cgcgGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGa                                                                                          <  1:54996/120‑1 (MQ=255)                                                          cgcgGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGa                                                                                          >  2:54996/1‑120 (MQ=255)                                                           gcggcgCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGc                                                                      >  1:697522/1‑139 (MQ=255)                                                            cggcgCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCg                                                                     >  1:744654/1‑139 (MQ=255)                                                             ggcgCTG‑TTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGtt                                                                   <  2:1348487/139‑1 (MQ=255)                                                               cgcTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTc                                                                  >  2:1216304/1‑139 (MQ=255)                                                                 cTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATggtgccagg                                                                                <  1:612977/123‑1 (MQ=255)                                                                 cTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATggtgccagg                                                                                >  2:612977/1‑123 (MQ=255)                                                                        tGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGtt                                                         <  1:135799/139‑1 (MQ=255)                                                                                             gTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGAcgcgc                                    <  1:1216304/139‑1 (MQ=255)                                                                                                 gTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCggg                                                                                                                                  <  1:950460/41‑1 (MQ=255)                                                                                                 gTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCggg                                                                                                                                  >  2:950460/1‑41 (MQ=255)                                                                                                 gTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGAcg                                                                                                                       >  1:1198737/1‑52 (MQ=255)                                                                                                 gTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGAcg                                                                                                                       <  2:1198737/52‑1 (MQ=255)                                                                                                 gTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACgcgc                                                                                                                    <  2:1497277/55‑1 (MQ=255)                                                                                                 gTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCTGCGGGCGATGTTGACgcgc                                                                                                                    >  1:1497277/1‑55 (MQ=255)                                                                                                                  gggaGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCgg                                                               >  2:959377/4‑91 (MQ=255)                                                                                                                  ggTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCgg                                                               <  1:959377/91‑1 (MQ=255)                                                                                                                  ggTAGTCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTc               >  1:795193/1‑139 (MQ=255)                                                                                                                       tCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGc                                                              >  2:1131599/1‑87 (MQ=255)                                                                                                                       tCGACGATAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGc                                                              <  1:1131599/87‑1 (MQ=255)                                                                                                                       tCGACGATAAAGCTGCGGGCCATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCAcgcg          >  2:164029/1‑139 (MQ=255)                                                                                                                           cgaTAAAGCTACGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCACGCGGAAc      >  1:826925/1‑139 (MQ=255)                                                                                                                             aTAAAGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCACGCGGAACGc    <  2:1266085/139‑1 (MQ=255)                                                                                                                               aaaGCTGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCACGCGGAACGCCg  <  2:697522/139‑1 (MQ=255)                                                                                                                               aaaGCTGCGGGCCATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCACGCGGAACGCCg  <  1:164029/139‑1 (MQ=255)                                                                                                                                    |                                                                                                                                      GAAGATGCCTACGATGGCTGCGCCACGGGTTTTGGCTTCGCGAATCAGTTCCACCACCGCGGCGCTGTTTTTGGCGTCCAGCGAGGCGGTAGGTTCGTCAAGCAGCAGAATGGGGTAGTCGACGATAAAGCCGCGGGCGATGTTGACGCGCTGCTGTTCGCCACCGGAAAATGTCGATGGTGCCAGGTGCCACAGGCGTTCCGGCACGTTCAGGCGGGTGAGAAGACGCGCGGCTTTAGCGGCGCAGGCTTCACGCGGAACGCCG  >  NC_000913/4317278‑4317542

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑