Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,467,233	A→G	Y230C (TAC→TGC)	intS →	CPS‑53 (KpLE1) prophage, putative prophage CPS‑53 integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,467,233	0	A	G	100.0%	190.5 / NA	52	Y230C (TAC→TGC)	intS	CPS‑53 (KpLE1) prophage, putative prophage CPS‑53 integrase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (28/24);  total (28/24)

GGGATACCGCAAGAAGAACTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTACACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCA  >  NC_000913/2467114‑2467362                                                                                                                        |                                                                                                                                  gggATACCGCAAGAAGAACTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGaaa                                                                                                                <  1:595919/139‑1 (MQ=255)      aCCGCAAGAAGAACTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCt                                                                                                           >  2:317326/1‑139 (MQ=255)          cAAGAAGAACTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGt                                                                                                       >  1:1146261/1‑139 (MQ=255)            agaagaACTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTc                                                                                                     >  2:871150/1‑139 (MQ=255)            agaagaACTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTc                                                                                                     >  1:1328644/1‑139 (MQ=255)              aagaaCTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCa                                                                                                   <  2:10848/139‑1 (MQ=255)                gaaCTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATg                                                                                                 <  2:1328644/139‑1 (MQ=255)                 aaCTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATg                                                                                                 <  1:40265/138‑1 (MQ=255)                 aaCTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATg                                                                                                 >  2:40265/1‑138 (MQ=255)                 aaCTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGc                                                                                                >  2:1228558/1‑139 (MQ=255)                           ttcttcCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTgca                                                                                                                                 >  1:917112/1‑96 (MQ=255)                                ccTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCg                                                                                 >  2:146072/1‑139 (MQ=255)                                    cAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGAttt                                                                             >  1:603290/1‑139 (MQ=255)                                         cAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCt                                                                                                           <  1:164355/104‑1 (MQ=255)                                         cAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCt                                                                                                           >  2:164355/1‑104 (MQ=255)                                            aTCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACC‑AAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAg                                                                    >  2:710663/1‑139 (MQ=255)                                              cccGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACC‑AAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGa                                                                  <  1:710663/139‑1 (MQ=255)                                                cGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGAt                                                                 >  2:175266/1‑139 (MQ=255)                                                 tgCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCAATTTTGAAAATAGGAtt                                                                >  1:828247/2‑139 (MQ=255)                                                     ttCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCa                                                            <  2:603290/139‑1 (MQ=255)                                                      tCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCAc                                                           >  1:22201/1‑139 (MQ=255)                                                      tCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCAc                                                           >  1:370851/1‑139 (MQ=255)                                                             aGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATg                                                                                                 >  2:111311/1‑94 (MQ=255)                                                             aGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATg                                                                                                 <  1:111311/94‑1 (MQ=255)                                                               cACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGtt                                                                                                      >  2:1153659/1‑87 (MQ=255)                                                               cACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGtt                                                                                                      <  1:1153659/87‑1 (MQ=255)                                                               cACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGc                                                  <  2:377456/139‑1 (MQ=255)                                                                aCTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGcc                                                 <  1:317326/139‑1 (MQ=255)                                                                 cTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCa                                                <  1:871150/139‑1 (MQ=255)                                                                  tGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAg                                               >  1:1237832/1‑139 (MQ=255)                                                                    gCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCt                                                                                                                          <  1:160746/62‑1 (MQ=255)                                                                    gCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCt                                                                                                                          >  2:160746/1‑62 (MQ=255)                                                                                            tcgCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCAtg                     <  2:22201/139‑1 (MQ=255)                                                                                            tcgCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCAtg                     >  2:669509/1‑139 (MQ=255)                                                                                            tcgCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCAtg                     <  2:1237832/139‑1 (MQ=255)                                                                                             cgCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGtt                                                                                                      >  2:1032549/1‑57 (MQ=255)                                                                                             cgCTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGtt                                                                                                      <  1:1032549/57‑1 (MQ=255)                                                                                               cTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCa                                                                                                   >  2:208581/1‑58 (MQ=255)                                                                                               cTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCa                                                                                                   <  1:546166/58‑1 (MQ=255)                                                                                               cTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCa                                                                                                   <  1:208581/58‑1 (MQ=255)                                                                                               cTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCa                                                                                                   >  2:546166/1‑58 (MQ=255)                                                                                               cTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGaaaa                                                                       >  2:200227/1‑86 (MQ=255)                                                                                               cTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGaaaa                                                                       <  1:200227/86‑1 (MQ=255)                                                                                               cTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCAtg                     >  1:427074/1‑136 (MQ=255)                                                                                               cTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCAtg                     <  2:427074/136‑1 (MQ=255)                                                                                               cTCATTGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTgg                  >  1:353639/1‑139 (MQ=255)                                                                                                   ttGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTcc              <  2:828247/139‑1 (MQ=255)                                                                                                    tGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGa                                                                  >  1:1049998/1‑86 (MQ=255)                                                                                                    tGCGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGa                                                                  <  2:1049998/86‑1 (MQ=255)                                                                                                      cGACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTAt           >  1:218039/1‑139 (MQ=255)                                                                                                       gACCAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATg          <  1:175266/139‑1 (MQ=255)                                                                                                         ccAAAGTTTTACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTc        >  2:1336713/1‑139 (MQ=255)                                                                                                               ttttACGCTGCACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCa  <  2:218039/139‑1 (MQ=255)                                                                                                                        |                                                                                                                                  GGGATACCGCAAGAAGAACTTCCCGTTTCTTCCTGCAGACCAGATCCCGGCATTCAACAAAGCACTGGCAACATTTTCAGGAAGTATCGTATCGCTCATTGCGACCAAAGTTTTACGCTACACAGCCCTAAGAACGAAAGAGCTTCGTTCCATGCTATGGAAGAACGTCGATTTTGAAAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCA  >  NC_000913/2467114‑2467362

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑