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%	221.2 / NA	62	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 (30/32);  total (30/32)

GGAGTGAGCGACCTTAACAACTATCGAATAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCTTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATCTATGTCGCGCATACAAA  >  NC_000913/2467696‑2467952                                                                                                                                        |                                                                                                                          ggAGTGAGCGACCTTAACAACTATCGAATAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTg                                                                                                                        >  2:229262/1‑139 (MQ=255) ggAGTGAGCGACCTTAACAACTATCGAATAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTg                                                                                                                        >  2:1249691/1‑139 (MQ=255)                      tATCGAATAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGaaa                                                                                                   >  1:350367/1‑139 (MQ=255)                      tATCGAATAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGaaa                                                                                                   >  2:343561/1‑139 (MQ=255)                               gCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGc                                                                                          >  2:687160/1‑139 (MQ=255)                                  caAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTAt                                                                                       >  2:850739/1‑139 (MQ=255)                                     aGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTg                                                                                    <  1:339509/139‑1 (MQ=255)                                       tCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCa                                                                                  <  2:1040539/139‑1 (MQ=255)                                            cAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTa                                                                             <  2:677434/139‑1 (MQ=255)                                             aaTCCAGTGTAAAGATTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTac                                                                            <  2:339200/139‑1 (MQ=255)                                             aaTCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTac                                                                            <  1:1109133/139‑1 (MQ=255)                                                   gTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTa                                                                             <  1:1463938/132‑1 (MQ=255)                                                   gTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTa                                                                             >  2:1463938/1‑132 (MQ=255)                                                   gTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACctct                                                                      >  1:409005/1‑139 (MQ=255)                                                     gCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTAt                                                                    <  1:1249691/139‑1 (MQ=255)                                                        aaGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTgg                                                                 >  2:293971/1‑139 (MQ=255)                                                         aGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCa                                                                                  >  2:458889/1‑121 (MQ=255)                                                         aGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCa                                                                                  <  1:458889/121‑1 (MQ=255)                                                         aGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATGATTAGCTGa                                                                                                            <  1:1029516/95‑1 (MQ=255)                                                         aGCTTTGTGTGTAAAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGa                                                                                                            >  2:1029516/1‑95 (MQ=255)                                                              tgtgtgTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCt                                                           >  1:781094/1‑139 (MQ=255)                                                                 gtgtATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                        <  1:343561/139‑1 (MQ=255)                                                                 gtgtATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                        <  2:781094/139‑1 (MQ=255)                                                                 gtgtATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                        <  1:850739/139‑1 (MQ=255)                                                                   gtATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAaca                                                      <  2:1161070/139‑1 (MQ=255)                                                                          ttttGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTtat                                               >  2:314077/1‑139 (MQ=255)                                                                             tGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATaca                                            <  1:350519/139‑1 (MQ=255)                                                                              gTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                        <  2:722642/126‑1 (MQ=255)                                                                              gTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                        <  2:106352/126‑1 (MQ=255)                                                                              gTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                        >  1:106352/1‑126 (MQ=255)                                                                              gTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                        >  1:722642/1‑126 (MQ=255)                                                                                   atcaACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACTCCCTTATACACTGggt                                      <  1:314077/139‑1 (MQ=255)                                                                                   atcaACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGggt                                      >  1:412073/1‑139 (MQ=255)                                                                                   atcaACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGggt                                      <  2:409005/139‑1 (MQ=255)                                                                                     caACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAGGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGggtgg                                    <  1:229262/139‑1 (MQ=255)                                                                                            aGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCa                                                                                  <  2:30414/86‑1 (MQ=255)                                                                                            aGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCa                                                                                  >  1:30414/1‑86 (MQ=255)                                                                                             gCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGt                                                                                                >  1:393724/1‑71 (MQ=255)                                                                                             gCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGt                                                                                                <  2:393724/71‑1 (MQ=255)                                                                                                   atcgatcgATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGt                      >  2:1167935/1‑139 (MQ=255)                                                                                                   atcgatcgATTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGt                      >  2:434059/1‑139 (MQ=255)                                                                                                      gatcgatTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCa                                                                                  <  1:4413/76‑1 (MQ=255)                                                                                                      gatcgatTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCa                                                                                  >  2:4413/1‑76 (MQ=255)                                                                                                      gatcgatTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTg                                                          >  2:130798/1‑100 (MQ=255)                                                                                                      gatcgatTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTg                                                          <  1:130798/100‑1 (MQ=255)                                                                                                      gatcgatTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAaca                                                      >  2:990582/1‑104 (MQ=255)                                                                                                      gatcgatTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAaca                                                      <  1:990582/104‑1 (MQ=255)                                                                                                        tcgatTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                        <  2:1479764/100‑1 (MQ=255)                                                                                                        tcgatTAAGACTTGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                        >  1:1479764/1‑100 (MQ=255)                                                                                                                    tGGATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATCTATGTCGCGCATAc     <  1:434059/139‑1 (MQ=255)                                                                                                                     ggATGATAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTAT‑‑ACTGGGTGGTTTTTGGTGTTTGTATCTATGTCGCGCATACaaa  >  1:485369/1‑139 (MQ=255)                                                                                                                      gatgatAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                        <  2:961696/86‑1 (MQ=255)                                                                                                                      gatgatAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGaa                                                        >  1:961696/1‑86 (MQ=255)                                                                                                                      gatgatAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATaca                                            >  2:182573/1‑98 (MQ=255)                                                                                                                      gatgatAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATaca                                            <  1:182573/98‑1 (MQ=255)                                                                                                                      gatgatAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGgt                            >  1:950722/1‑114 (MQ=255)                                                                                                                      gatgatAGACTTCATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGgt                            <  2:950722/114‑1 (MQ=255)                                                                                                                                  cATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAaca                                                      <  2:234732/76‑1 (MQ=255)                                                                                                                                  cATTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAaca                                                      >  1:234732/1‑76 (MQ=255)                                                                                                                                   aTTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATCTATGTcg            <  2:126094/117‑1 (MQ=255)                                                                                                                                   aTTCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATCTATGTcg            >  1:126094/1‑117 (MQ=255)                                                                                                                                     tCCCTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGtgtg                                                             <  2:386104/66‑1 (MQ=255)                                                                                                                                        |                                                                                                                          GGAGTGAGCGACCTTAACAACTATCGAATAGCACAAAGTCTTGCAATCCAGTGCAAAGCTTTGTGTGTATAAGTTTTGTCTCATCAACCACAGCAAGTATCGATCGATTAAGACTTGGATGATAGACTTCATTCCTTTGATTATTAGCTGATAGAAGAAATGTTAAAGCTATTTGCAAAGTACACCTCTATTGGTGTGCTGAACACCCTTATACACTGGGTGGTTTTTGGTGTTTGTATCTATGTCGCGCATACAAA  >  NC_000913/2467696‑2467952

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑