Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	790,778	G→A	intergenic (+277/‑197)	kipA_1 → / → ltaS	KipI antagonist/Lipoteichoic acid synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	790,778	0	G	A	100.0%	204.6 / NA	60	intergenic (+277/‑197)	kipA_1/ltaS	KipI antagonist/Lipoteichoic acid synthase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (26/34);  total (26/34)

ACTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTAA  >  USA300TCH1516_ALE/790643‑790914                                                                                                                                        |                                                                                                                                         aCTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAATTATGAGTTATAGCCCAAAATa                                                                                                                              <  1:533382/148‑1 (MQ=255) aCTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATa                                                                                                                              <  1:39507/148‑1 (MQ=255)  cTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTCCAATTCGCCGACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATAc                                                                                                                             <  1:972482/148‑1 (MQ=255)  attGAATTTAGACTAAAATTACTCTATATTTATTAATTGAGATATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTCAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATAc                                                                                                                             <  2:606992/147‑1 (MQ=255)     gAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTg                                                                                                                          >  2:964179/1‑148 (MQ=255)      aaTTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGt                                                                                                                         <  1:74558/148‑1 (MQ=255)       aTTTTGACTAAAATTACTCTATATTTATTAATTGAGTTATGCTTATTAGTACAATTTGATTACATTTTTTAAATTTTTTATTTGAATGATGATATTAAATAAAGAATCTTACACAAGTAAATATATGTTATAGCTCAAAATACTTGtt                                                                                                                        >  1:454669/1‑148 (MQ=255)       aTTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGtt                                                                                                                        <  2:289108/148‑1 (MQ=255)       aTTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATGACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGtt                                                                                                                        >  2:729348/1‑148 (MQ=255)       aTTTTGACTAAAATTACTCTATATTTATTAATTCAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAAGTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGtt                                                                                                                        <  2:555854/148‑1 (MQ=255)         tttGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTaa                                                                                                                      <  2:691167/148‑1 (MQ=255)         tttGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTaa                                                                                                                      <  1:629145/148‑1 (MQ=255)         tttGAATAAAACTACTTTATATTTATTAATGGAGCTATGCTGTTTATTATAATTTGATTACAAATTTTAAATTTGCTAATTGAATGATAATATTAAATAAAGCAACTGACACAAGCAAATATGCCTTATAGCCCAAAATACTTGTTaa                                                                                                                      <  2:132114/148‑1 (MQ=255)             aCTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCa                                                                                                                  <  2:772383/148‑1 (MQ=255)              cTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCaa                                                                                                                 <  1:60148/148‑1 (MQ=255)                 aaaTTACTCTATATTTATTAAGTGAGCTGTGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATAGTAAATAAAGAAATTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGt                                                                                                              >  2:679904/1‑148 (MQ=255)                  aaTTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGtt                                                                                                             <  1:414909/148‑1 (MQ=255)                     tACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGaa                                                                                                          <  2:378893/148‑1 (MQ=255)                     tACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGaa                                                                                                          <  2:837044/148‑1 (MQ=255)                            tatttattAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACa                                                                                                   <  2:110669/148‑1 (MQ=255)                            tatttattAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACa                                                                                                   >  1:827724/1‑148 (MQ=255)                                tattaATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATa                                                                                               <  2:278837/148‑1 (MQ=255)                                tattaATTGAGCTAAGCTTATTATTAAAATTTGATTAAAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATa                                                                                               <  1:115996/148‑1 (MQ=255)                                 attaattaAGCTTTGTTTATTTATACATATTAAATACAAATTTGAAATTTGTTAATTTAATAATCATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATATCCCAAAATACTTTTTAAATCAAAGTTGAAAGCTACAAAGaa                                                                                              <  2:320871/148‑1 (MQ=255)                                          gCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATta                                                                                     >  2:110975/1‑148 (MQ=255)                                                 ttattattaCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACtt                                                                              >  1:82635/1‑148 (MQ=255)                                                 ttattattaCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAAAtt                                                                              >  1:45059/1‑148 (MQ=255)                                                    ttattaCAATTTGATTAAAAATTTGAAATTTGTTAATTGAATGATAATAAAAAATAAAGAAACTTAGACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAGATCGAGGTTGGAAGCTACAAATAACGAAAATTATAAACTTGaa                                                                           <  2:937074/148‑1 (MQ=255)                                                            aTTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAACGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAg                                                                   <  2:362517/148‑1 (MQ=255)                                                             tttGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGt                                                                  >  1:173369/1‑148 (MQ=255)                                                                 aTTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAAtt                                                              <  1:28222/148‑1 (MQ=255)                                                                      aaaTTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGTAACCAACAAAGAACGCACATTATAAACTTGAATCTGAAAGTAGTTACtat                                                         >  1:469987/1‑148 (MQ=255)                                                                      aaaTTTTAAATGTGTTAATGGAATGATAATATTAGATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACtat                                                         >  1:701825/1‑148 (MQ=255)                                                                                   gTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATg                                            <  2:416365/148‑1 (MQ=255)                                                                                      aaTTGAATGATAATATTAAATAAAGACACTTACAGAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTa                                         >  1:482824/1‑148 (MQ=255)                                                                                      aaTTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTa                                         >  2:723709/1‑148 (MQ=255)                                                                                           aaTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACttt                                    <  1:965033/148‑1 (MQ=255)                                                                                           aaTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACttt                                    <  1:537875/148‑1 (MQ=255)                                                                                            aTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAACATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACtttt                                   <  2:546410/148‑1 (MQ=255)                                                                                            aTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATACTTATGACAATGTTAACtttt                                   >  1:268276/1‑148 (MQ=255)                                                                                            aTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACtttt                                   >  2:199801/1‑148 (MQ=255)                                                                                            aTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACtttt                                   >  2:442822/1‑148 (MQ=255)                                                                                                      taaataaaGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACtt                         <  1:901357/148‑1 (MQ=255)                                                                                                      taaataaaGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACtt                         <  1:883502/148‑1 (MQ=255)                                                                                                      taaataaaGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACtt                         <  1:414163/148‑1 (MQ=255)                                                                                                            aaGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTattaat                   <  2:539980/148‑1 (MQ=255)                                                                                                             aGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTATATTTAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTCCTATCATTATGAAAATGTTAACTTTTAAAAGCACTTattaatt                  >  1:681805/1‑148 (MQ=255)                                                                                                             aGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTattaatt                  >  2:123365/1‑148 (MQ=255)                                                                                                             aGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTattaatt                  >  1:294764/1‑148 (MQ=255)                                                                                                              gAAACTTACAGAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAGAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTattaatta                 >  1:713924/1‑148 (MQ=255)                                                                                                               aaaCTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTAttaattaa                >  1:912633/1‑148 (MQ=255)                                                                                                               aaaCTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTAttaattaa                <  1:15919/148‑1 (MQ=255)                                                                                                                aaCTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATCACGAAAATTATAAACTTGAATCTAAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAAAGCACTTATTAATTAAc               >  1:804475/1‑148 (MQ=255)                                                                                                                aaCTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAAc               >  1:756937/1‑148 (MQ=255)                                                                                                                   ttACACAAGCAAATATGAATTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTCAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTAc            <  1:776479/148‑1 (MQ=255)                                                                                                                    tACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACCGTCTTAACTTTTAAACGCACTTATTAATTAACTACa           <  1:729348/148‑1 (MQ=255)                                                                                                                     acacAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACAt          >  1:820262/1‑148 (MQ=255)                                                                                                                       acaAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATaa        <  1:110975/148‑1 (MQ=255)                                                                                                                          aGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGt     >  2:505538/1‑148 (MQ=255)                                                                                                                             aaaTATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTAAATAATGTTaa  >  2:868349/1‑148 (MQ=255)                                                                                                                                        |                                                                                                                                         ACTTGAATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTAA  >  USA300TCH1516_ALE/790643‑790914

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑