Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,232,053	A→T	D233V (GAT→GTT)	stp →	Serine/threonine phosphatase stp

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,232,053	0	A	T	100.0%	203.7 / NA	56	D233V (GAT→GTT)	stp	Serine/threonine phosphatase stp
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (33/23);  total (33/23)

TGATTATTTATTATTAAATTCAGATGGATTAACTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGATAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTA  >  USA300TCH1516_ALE/1231913‑1232198                                                                                                                                              |                                                                                                                                                  tGATTATTTATTATTAAATTCAGATGGATTAACTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTAAAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACt                                                                                                                                         >  4:158129/1‑151 (MQ=255)  gATTATTTATTATTAAATTCAGATGGATTAACTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACtt                                                                                                                                        <  1:736496/151‑1 (MQ=255)     tatttattATTAAATTCAGATGGATTAACTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCa                                                                                                                                     <  1:318088/151‑1 (MQ=255)             attaAATTCAGATGGATTAACTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTcgcg                                                                                                                             >  1:134015/1‑151 (MQ=255)             attaAATTCAGATGGATTAACTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTcgcg                                                                                                                             >  1:449881/1‑151 (MQ=255)                     cAGATGGATTAACTGATTATGTTAAANACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGa                                                                                                                     >  3:305026/1‑151 (MQ=255)                       gATGGATTAACTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAg                                                                                                                   >  1:548535/1‑151 (MQ=255)                        aTGGATTAACTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATCCTCGCGGCTATTGAAgg                                                                                                                  <  2:483594/151‑1 (MQ=255)                        aTGGATTAACTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAgg                                                                                                                  <  2:529795/151‑1 (MQ=255)                                 cTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGt                                                                                                         >  3:295607/1‑151 (MQ=255)                                 cTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGt                                                                                                         >  1:29706/1‑151 (MQ=255)                                  tGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTa                                                                                                        >  3:209224/1‑151 (MQ=255)                                  tGATTATGTTAAAGACAATGAAATTAAGCGATTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTa                                                                                                        >  2:973785/1‑151 (MQ=255)                                     ttATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGa                                                                                                     <  2:768112/151‑1 (MQ=255)                                        tGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAg                                                                                                  >  2:376834/1‑151 (MQ=255)                                         gtcaaaGACAATGAAATTAAGCATTTGTTAGTAAAAGAAGGTACCATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAgg                                                                                                 <  1:890793/148‑1 (MQ=255)                                         gTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAgg                                                                                                 >  3:256487/1‑151 (MQ=255)                                          ttAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGt                                                                                                >  2:299134/1‑151 (MQ=255)                                               gACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAaat                                                                                           <  3:154254/151‑1 (MQ=255)                                                   aTGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAataata                                                                                       >  2:541950/1‑151 (MQ=255)                                                       aaTTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATg                                                                                   <  1:745445/151‑1 (MQ=255)                                                               gTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGatat                                                                           <  1:716402/151‑1 (MQ=255)                                                                   gTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATaaaa                                                                       >  2:837247/1‑151 (MQ=255)                                                                    ttAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAAt                                                                      <  2:425128/151‑1 (MQ=255)                                                                      aGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTg                                                                    <  2:211295/151‑1 (MQ=255)                                                                       gTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGt                                                                   >  2:460795/1‑151 (MQ=255)                                                                         aaaaGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAg                                                                 >  2:883337/1‑151 (MQ=255)                                                                         aaaaGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAg                                                                 <  1:802098/151‑1 (MQ=255)                                                                               agGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGc                                                           >  1:1595/1‑151 (MQ=255)                                                                                ggTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCt                                                          >  1:430874/1‑151 (MQ=255)                                                                                 gTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCtt                                                         >  4:358096/1‑151 (MQ=255)                                                                                    cAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTggc                                                      <  1:48662/151‑1 (MQ=255)                                                                                    cAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTggc                                                      <  1:54004/151‑1 (MQ=255)                                                                                         gaagaTCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTCTTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGCTAAGCTTGGcggcgg                                                 >  2:481867/1‑151 (MQ=255)                                                                                         gaagaTCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGcggcgg                                                 >  2:961233/1‑151 (MQ=255)                                                                                                        cAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGt                                  <  1:620910/151‑1 (MQ=255)                                                                                                         aaTTAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGtt                                 <  2:449881/151‑1 (MQ=255)                                                                                                          tctAATGCCAATT‑GCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGttt                                >  3:186115/3‑151 (MQ=255)                                                                                                           ttAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTa                               <  4:256487/151‑1 (MQ=255)                                                                                                            tAATG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTAt                              >  4:198310/1‑151 (MQ=255)                                                                                                             aaTG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATc                             <  4:26161/151‑1 (MQ=255)                                                                                                              aTG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCt                            >  4:175061/1‑151 (MQ=255)                                                                                                              aTG‑CAATTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCt                            >  1:900108/1‑151 (MQ=255)                                                                                                                    aTTGGCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTg                       <  1:376834/151‑1 (MQ=255)                                                                                                                        gCATTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAga                   <  1:541950/151‑1 (MQ=255)                                                                                                                          aTTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAgata                 >  1:704059/1‑151 (MQ=255)                                                                                                                          aTTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAgata                 >  3:124258/1‑151 (MQ=255)                                                                                                                          aTTAGATAACCATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAgata                 <  2:65867/151‑1 (MQ=255)                                                                                                                                   ccATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGATGAAGATACGATACTTa        >  3:188221/1‑151 (MQ=255)                                                                                                                                    cATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTaa       >  3:298552/1‑151 (MQ=255)                                                                                                                                    cATTCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTaa       >  2:477151/1‑151 (MQ=255)                                                                                                                                       tCGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACAt    <  2:156574/151‑1 (MQ=255)                                                                                                                                        cGAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACAtt   >  2:329234/1‑151 (MQ=255)                                                                                                                                         gAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATTATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTa  >  2:914053/1‑151 (MQ=255)                                                                                                                                         gAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAaataa                                                                                         <  1:787352/64‑1 (MQ=255)                                                                                                                                         gAAAGTTAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAaataa                                                                                         >  2:787352/1‑64 (MQ=255)                                                                                                                                              |                                                                                                                                                  TGATTATTTATTATTAAATTCAGATGGATTAACTGATTATGTTAAAGACAATGAAATTAAGCGTTTGTTAGTAAAAGAAGGTACAATAGAAGATCATGGTGATCAATTAATG‑CAATTGGCATTAGATAACCATTCGAAAGATAACGTTACTTTCATACTCGCGGCTATTGAAGGTGATAAAGTATGATAGGTAAAATAATAAATGAACGATATAAAATTGTAGATAAGCTTGGCGGCGGTGGCATGAGTACCGTTTATCTTGCTGAAGATACGATACTTAACATTA  >  USA300TCH1516_ALE/1231913‑1232198

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑