Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,467,831	T→C	intergenic (+129/‑24)	intS → / → gtrA	CPS‑53 (KpLE1) prophage, putative prophage CPS‑53 integrase/CPS‑53 (KpLE1) prophage, bactoprenol‑linked glucose translocase/flippase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,467,831	0	T	C	100.0%	199.4 / NA	55	intergenic (+129/‑24)	intS/gtrA	CPS‑53 (KpLE1) prophage, putative prophage CPS‑53 integrase/CPS‑53 (KpLE1) prophage, bactoprenol‑linked glucose translocase/flippase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (26/29);  total (26/29)

CGACCTTAACAACTATCGAATAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCTTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATCTATGTCGCGCATACAAACCAAGCTCTT  >  NC_000913/2467704‑2467962                                                                                                                                |                                                                                                                                    cGACCTTAACAACTATCGAATAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAg                                                                                                                          <  1:818127/139‑1 (MQ=255)            acTATCGAATAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATagaaga                                                                                                               <  2:1473567/139‑1 (MQ=255)                   aaTAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTa                                                                                                        <  2:1454703/139‑1 (MQ=255)                     tAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTaaa                                                                                                      <  2:1335903/139‑1 (MQ=255)                       gCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGc                                                                                                    >  1:980970/1‑139 (MQ=255)                                  tGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAg                                                                                         >  2:510770/1‑139 (MQ=255)                                     aaTCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCGTTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTac                                                                                      <  1:178402/139‑1 (MQ=255)                                         cAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGatt                                                                                                                               >  2:288156/1‑94 (MQ=255)                                         cAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGatt                                                                                                                               <  1:288156/94‑1 (MQ=255)                                           gTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACctct                                                                                >  1:1431207/1‑139 (MQ=255)                                                 aGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCa                                                                                            <  1:986851/121‑1 (MQ=255)                                                 aGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGAATAAGACTTGGATGATAGACTTCATACCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCa                                                                                            >  2:986851/1‑121 (MQ=255)                                                      tgtgtgTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGc                                                                                                                         <  2:902379/87‑1 (MQ=255)                                                      tgtgtgTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGc                                                                                                                         >  1:902379/1‑87 (MQ=255)                                                      tgtgtgTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTacac                                                                                    >  2:781444/1‑124 (MQ=255)                                                      tgtgtgTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTacac                                                                                    <  1:781444/124‑1 (MQ=255)                                                      tgtgtgTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCt                                                                     >  2:1125616/1‑139 (MQ=255)                                                         gtgtATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                                  <  1:405143/139‑1 (MQ=255)                                                         gtgtATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                                  <  1:510770/139‑1 (MQ=255)                                                         gtgtATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                                  <  1:605254/139‑1 (MQ=255)                                                         gtgtATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                                  <  2:980970/139‑1 (MQ=255)                                                           gtATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAaca                                                                <  2:887630/139‑1 (MQ=255)                                                                      gTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGGAGAAATGTTAAAGCTATTTGCAAAGTac                                                                                      <  2:998861/106‑1 (MQ=255)                                                                      gTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTac                                                                                      >  1:998861/1‑106 (MQ=255)                                                                      gTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATacac                                                     >  2:1281469/1‑139 (MQ=255)                                                                      gTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATacac                                                     >  2:432890/1‑139 (MQ=255)                                                                           atcaACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGggt                                                <  2:1431207/139‑1 (MQ=255)                                                                            tcaACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTg                                                                            <  1:678258/110‑1 (MQ=255)                                                                            tcaACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTg                                                                            >  2:678258/1‑110 (MQ=255)                                                                                        aGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGtt                                   <  2:923922/139‑1 (MQ=255)                                                                                           atcgatcgATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATagaaga                                                                                                               <  1:971688/60‑1 (MQ=255)                                                                                           atcgatcgATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATagaaga                                                                                                               >  2:971688/1‑60 (MQ=255)                                                                                              gatcgatTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATc                             >  2:1269386/1‑139 (MQ=255)                                                                                              gatcgatTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATc                             >  2:43993/1‑139 (MQ=255)                                                                                               atcgatTAAGACTTGGATGATAGACTTCGTTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                                  >  1:358992/1‑101 (MQ=255)                                                                                               atcgatTAAGACTTGGATGATAGACTTCGTTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                                  <  2:358992/101‑1 (MQ=255)                                                                                                    ttAAGACTTGGATGATAGGCTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGggt                                                <  1:1046769/114‑1 (MQ=255)                                                                                                    ttAAGACTGGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGggt                                                >  2:1046769/1‑114 (MQ=255)                                                                                                     tAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATCTATGTcg                      <  1:432890/139‑1 (MQ=255)                                                                                                             ggATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCa                                                                                            <  2:77096/61‑1 (MQ=255)                                                                                                             ggATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCa                                                                                            >  1:77096/1‑61 (MQ=255)                                                                                                             ggATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTAt                                                                              <  2:702749/75‑1 (MQ=255)                                                                                                             ggATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTAt                                                                              >  1:702749/1‑75 (MQ=255)                                                                                                              gatgatAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGtt                                            >  2:279480/1‑108 (MQ=255)                                                                                                              gatgatAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGtt                                            <  1:279480/108‑1 (MQ=255)                                                                                                              gatgatAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGtt                                   >  2:615846/1‑117 (MQ=255)                                                                                                              gatgatAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGtt                                   <  1:615846/117‑1 (MQ=255)                                                                                                                   tAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                                  <  1:370321/81‑1 (MQ=255)                                                                                                                   tAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                                  >  2:370321/1‑81 (MQ=255)                                                                                                                   tAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGtt                                   <  2:1477332/112‑1 (MQ=255)                                                                                                                   tAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGtt                                   >  1:1477332/1‑112 (MQ=255)                                                                                                                     gACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATCTATGTCGCGCATACAAACCAAGc      >  1:447905/1‑139 (MQ=255)                                                                                                                        ttCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGt                                                                                        >  2:151299/1‑54 (MQ=255)                                                                                                                        ttCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGt                                                                                        <  1:151299/54‑1 (MQ=255)                                                                                                                         tCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATCTATGTCGCGCATACAAACCAAGCTCtt  >  2:33622/1‑139 (MQ=255)                                                                                                                                |                                                                                                                                    CGACCTTAACAACTATCGAATAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCTTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATCTATGTCGCGCATACAAACCAAGCTCTT  >  NC_000913/2467704‑2467962

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑