Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,386,119	G→A	P114L (CCG→CTG)	USA300HOU_2245 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,386,119	0	G	A	100.0%	203.2 / NA	56	P114L (CCG→CTG)	USA300HOU_2245	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (34/22);  total (34/22)

AGTACGCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTCCGCCT  >  CP000730/2385986‑2386253                                                                                                                                       |                                                                                                                                       aGTACGCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCctac                                                                                                                                 <  1:163660/141‑1 (MQ=255)         tGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCaa                                                                                                                         <  2:584364/141‑1 (MQ=255)            aaTCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCt                                                                                                                      <  1:780300/141‑1 (MQ=255)               cACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATACAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCt                                                                                                                   >  2:322090/1‑141 (MQ=255)                 cTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCa                                                                                                                 >  1:547121/1‑141 (MQ=255)                     cttcCCATTGAATAAAAAATGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACttt                                                                                                             <  1:839422/141‑1 (MQ=255)                       tcCCATTGAATAAAAAATGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGt                                                                                                           <  1:292163/141‑1 (MQ=255)                        cccATTGAATAAACAGTGGTGGCTTGATTT‑ATGACTTAGCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTa                                                                                                          <  1:815787/141‑1 (MQ=255)                          cATTGAATAAAAAATGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGt                                                                                                        >  2:89549/1‑141 (MQ=255)                                 tAAAAAATGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTAtttt                                                                                                 <  2:742373/141‑1 (MQ=255)                                     aaaTGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTTGTTTCTTTTTatg                                                                                             >  2:467148/1‑139 (MQ=255)                                     aaaTGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAAc                                                                                             <  1:348136/141‑1 (MQ=255)                                        tggtggCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGc                                                                                          >  2:797294/1‑141 (MQ=255)                                          gtggCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCct                                                                                        >  2:367108/1‑141 (MQ=255)                                           tggCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCctc                                                                                       >  1:335765/1‑141 (MQ=255)                                            ggCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCctct                                                                                      >  1:629849/1‑141 (MQ=255)                                              cTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCtat                                                                                    <  2:855303/141‑1 (MQ=255)                                                        tca‑tcatcCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTa                                                                          >  2:594529/1‑141 (MQ=255)                                                        tca‑tcatcCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTa                                                                          >  2:68717/1‑141 (MQ=255)                                                         ca‑tcatcCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTAc                                                                         <  2:95295/141‑1 (MQ=255)                                                             catcCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGca                                                                      >  1:576554/1‑141 (MQ=255)                                                              atcCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGcaa                                                                     <  1:509581/141‑1 (MQ=255)                                                                  tGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGcaaacaa                                                                 <  2:56311/141‑1 (MQ=255)                                                                     ttCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAata                                                              >  2:317869/1‑141 (MQ=255)                                                                     ttCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAata                                                              >  2:318000/1‑141 (MQ=255)                                                                       cATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAtt                                                            <  1:159840/141‑1 (MQ=255)                                                                       cATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAtt                                                            >  1:595019/1‑141 (MQ=255)                                                                        aTTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCACTTTCCATTTGAATCAGCCCTACTCCTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAttt                                                           >  2:416509/1‑141 (MQ=255)                                                                          tatataAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATAttttt                                                         >  1:755839/1‑141 (MQ=255)                                                                            tataAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTaa                                                       >  1:363831/1‑141 (MQ=255)                                                                            tataAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTaa                                                       <  1:854063/141‑1 (MQ=255)                                                                                aaGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGcc                                                   <  1:421358/141‑1 (MQ=255)                                                                                 aGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCt                                                  >  1:66760/1‑141 (MQ=255)                                                                                  gCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAACTATTTTTAAAGCCtt                                                 >  1:716988/1‑141 (MQ=255)                                                                                      ttGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTc                                             <  1:533365/141‑1 (MQ=255)                                                                                      ttGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTc                                             >  2:41430/1‑141 (MQ=255)                                                                                        gCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCAt                                           >  1:460132/1‑141 (MQ=255)                                                                                              ttaccttaccATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTtct                                     >  1:845706/1‑141 (MQ=255)                                                                                                   ttaccATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGa                                <  1:291348/141‑1 (MQ=255)                                                                                                   ttaccATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGa                                <  1:267287/141‑1 (MQ=255)                                                                                                   ttaccATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGa                                >  2:476745/1‑141 (MQ=255)                                                                                                      ccATCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACa                             >  2:715950/1‑141 (MQ=255)                                                                                                        aTCTTTATGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAAt                           <  1:132618/141‑1 (MQ=255)                                                                                                              aTGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGt                     >  2:333479/1‑141 (MQ=255)                                                                                                              aTGTGTATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGt                     <  1:377109/141‑1 (MQ=255)                                                                                                                gtgtATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTCTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAg                   >  1:639763/1‑141 (MQ=255)                                                                                                                 tgtAGCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACCTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAATTATTTTTAAAGCCTTGCTCATATTTCTCTTGAACAATTTAAGTAga                  >  2:860333/1‑140 (MQ=255)                                                                                                                  gtATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCa                                            <  1:400395/114‑1 (MQ=255)                                                                                                                  gtATCTCTTTCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCa                                            >  2:400395/1‑114 (MQ=255)                                                                                                                         tttCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGa          >  2:176513/1‑141 (MQ=255)                                                                                                                         tttCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGa          >  1:494574/1‑141 (MQ=255)                                                                                                                           tCCATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACt        >  1:115358/1‑141 (MQ=255)                                                                                                                            ccATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTc       >  2:261081/1‑141 (MQ=255)                                                                                                                            ccATTTGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTc       <  1:513232/141‑1 (MQ=255)                                                                                                                                ttGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTCCGcc   >  1:4436/1‑141 (MQ=255)                                                                                                                                 tGAATCAGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTCCGCCt  >  1:45526/1‑141 (MQ=255)                                                                                                                                       |                                                                                                                                       AGTACGCATGGAATCACTTTCTTCCCATTGAATAAAAAATGGTGGCTTAATTTCATCA‑TCATCCTGATTCATTATATAAAGCAATTGCCACTTTACCTTACCATCTTTATGTGTATCTCTTTCCATTTGAATCGGCCCTACTACTTCAACCTGCTCACTTTGTAGTTTATTTTTAACTGCCTCTATATCATTTGTACGCAAACAAATATTTTTAAAGCCTTGCTCATACTTCTCTTGAACAATTTGAGTAGCAAAAGCGACTCCGCCT  >  CP000730/2385986‑2386253

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑