Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,042,775	C→T	R479H (CGC→CAC)	etk ←	tyrosine‑protein kinase, role in O‑antigen capsule formation

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,042,775	0	C	T	100.0%	168.6 / NA	52	R479H (CGC→CAC)	etk	tyrosine‑protein kinase, role in O‑antigen capsule formation
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (25/27);  total (25/27)

GTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGCGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAACAGGCC  >  NC_000913/1042652‑1042908                                                                                                                            |                                                                                                                                      gTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAg                                                                                                                             >  2:966849/1‑134 (MQ=255) gTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAg                                                                                                                             <  1:966849/134‑1 (MQ=255)                        cacaGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGc                                                                                                                            <  1:1079353/112‑1 (MQ=255)                        cacaGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGc                                                                                                                            >  2:1079353/1‑112 (MQ=255)                             cagAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCa                                                                                                                              <  2:1567588/105‑1 (MQ=255)                             cagAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCa                                                                                                                              >  1:1567588/1‑105 (MQ=255)                                      ccgGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTg                                                                                   <  2:486587/139‑1 (MQ=255)                                       cgGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc                                                                                  >  2:21274/1‑139 (MQ=255)                                       cgGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc                                                                                  <  1:21274/139‑1 (MQ=255)                                          gTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCAGCTGATTAGAAAATAAATTTTTCATACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGctct                                                                               <  1:533933/139‑1 (MQ=255)                                                        ggAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAg                                                                                                                             >  1:743319/1‑79 (MQ=255)                                                        ggAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAg                                                                                                                             <  2:743319/79‑1 (MQ=255)                                                             gggATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCtt                                                            >  1:310064/1‑139 (MQ=255)                                                                        aGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGAc                                                                                                                   >  1:320011/1‑73 (MQ=255)                                                                        aGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGAc                                                                                                                   <  2:320011/73‑1 (MQ=255)                                                                               tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGa                                                                                                                    <  1:89761/65‑1 (MQ=255)                                                                               tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGa                                                                                                                    >  2:89761/1‑65 (MQ=255)                                                                               tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGTCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACa                                          >  1:1142988/1‑139 (MQ=255)                                                                               tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTg                                                                                   <  1:877059/98‑1 (MQ=255)                                                                               tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTg                                                                                   >  2:877059/1‑98 (MQ=255)                                                                               tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc                                                                                  <  2:1111163/99‑1 (MQ=255)                                                                               tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc                                                                                  >  1:1111163/1‑99 (MQ=255)                                                                               tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg                                                                 <  1:502121/116‑1 (MQ=255)                                                                               tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg                                                                 >  2:502121/1‑116 (MQ=255)                                                                                       ctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg                                                                 <  2:171130/108‑1 (MQ=255)                                                                                       ctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg                                                                 >  1:171130/1‑108 (MQ=255)                                                                                          aTTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGcc                               >  2:1024948/1‑139 (MQ=255)                                                                                                 aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACt                                                                                                                        >  2:1336638/1‑43 (MQ=255)                                                                                                 aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACt                                                                                                                        <  1:1336638/43‑1 (MQ=255)                                                                                                 aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACa                                                                                                                  >  2:613865/1‑49 (MQ=255)                                                                                                 aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACa                                                                                                                  <  1:613865/49‑1 (MQ=255)                                                                                                 aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGa                                                                                                            >  1:1571664/1‑55 (MQ=255)                                                                                                 aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGa                                                                                                            <  2:1571664/55‑1 (MQ=255)                                                                                                 aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGTCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACgg                        <  2:1142988/139‑1 (MQ=255)                                                                                                 aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGctct                                                                               >  2:368276/1‑84 (MQ=255)                                                                                                 aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGctct                                                                               <  1:368276/84‑1 (MQ=255)                                                                                                 aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg                                                                 <  1:1391979/98‑1 (MQ=255)                                                                                                 aataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg                                                                 >  2:1391979/1‑98 (MQ=255)                                                                                                  ataaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGc                       <  2:310064/139‑1 (MQ=255)                                                                                                    aaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg                                                                 <  1:594413/95‑1 (MQ=255)                                                                                                    aaatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCgg                                                                 >  2:594413/1‑95 (MQ=255)                                                                                                         tttCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCa                                     >  1:817551/1‑118 (MQ=255)                                                                                                         tttCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCa                                     <  2:817551/118‑1 (MQ=255)                                                                                                             ttACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAACACGGc                       >  1:1351083/1‑128 (MQ=255)                                                                                                             ttACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAACACGGc                       <  2:1351083/128‑1 (MQ=255)                                                                                                                     aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCca                  >  1:1204331/1‑125 (MQ=255)                                                                                                                     aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCca                  <  2:1204331/125‑1 (MQ=255)                                                                                                                     aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAAc       <  2:857862/136‑1 (MQ=255)                                                                                                                     aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAAc       >  1:857862/1‑136 (MQ=255)                                                                                                                      cGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAACAGGc   >  2:1507269/1‑139 (MQ=255)                                                                                                                       gggTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAACAGGcc  <  1:1507269/139‑1 (MQ=255)                                                                                                                       gggTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAACAGGcc  <  1:1024948/139‑1 (MQ=255)                                                                                                                            |                                                                                                                                      GTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGCGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACCCACAGAAATAAACAGGCC  >  NC_000913/1042652‑1042908

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: ‑