Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,027,751	C→G	100%	V66L (GTA→CTA)	vraS ←	Sensor protein VraS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,027,751	0	C	G	100.0%	217.6 / NA	62	V66L (GTA→CTA)	vraS	Sensor protein VraS
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (36/26);  total (36/26)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATG  >  USA300TCH1516_ALE/2027620‑2027885                                                                                                                                    |                                                                                                                                       ttGGTATAAATCTAACGTTTCACTATCTTTGTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACcaac                                                                                                                               <  2:534338/140‑1 (MQ=255) agagcataAATCTAACCTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGATCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACcaac                                                                                                                               <  2:189865/136‑1 (MQ=255)           tCTAACGTTTCACTATATATTTCTATATTTTGATCATTCATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATacac                                                                                                                     >  2:318833/1‑141 (MQ=255)            cTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATAcaca                                                                                                                    >  2:500849/1‑141 (MQ=255)            cTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCACCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATAcaca                                                                                                                    <  1:364016/141‑1 (MQ=255)              aaCGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACaat                                                                                                                  >  1:556447/1‑141 (MQ=255)              aaCGTTTCACTATATATTTCGATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGCGTAGCGAACCAACAATAATACACaaa                                                                                                                  >  1:421431/1‑140 (MQ=255)                       cTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTACGTCTTAATCCAATCATTTTGCTGATGGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATatgatg                                                                                                         >  1:288548/1‑141 (MQ=255)                        tatataTTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATATATATTATTatgatgg                                                                                                        >  1:50956/1‑140 (MQ=255)                           atatTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATAtgatgatga                                                                                                     <  2:384538/141‑1 (MQ=255)                             atTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATgaga                                                                                                   <  1:76133/141‑1 (MQ=255)                               ttCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGAtt                                                                                                 >  1:382237/1‑141 (MQ=255)                                    tatTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaa                                                                                            >  1:519995/1‑141 (MQ=255)                                     atTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaa                                                                                           <  1:242511/141‑1 (MQ=255)                                     atTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaa                                                                                           <  1:370804/141‑1 (MQ=255)                                     atTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAAGAATACACAATAATATGAGGATGAGATTtaaaaa                                                                                           >  1:12080/1‑141 (MQ=255)                                      ttttGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaat                                                                                          >  1:133789/1‑141 (MQ=255)                                            tCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaa                                                                                           <  2:500456/134‑1 (MQ=255)                                            tCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaa                                                                                           >  1:500456/1‑134 (MQ=255)                                               ttAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGTTTTAAAAATAAAAAAACt                                                                                 >  2:267903/1‑141 (MQ=255)                                               ttAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAcc                                                                                 >  2:32253/1‑140 (MQ=255)                                               ttAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGAGGATGAGATTTACAAATAAAAAAACt                                                                                 >  2:373937/1‑141 (MQ=255)                                                 aaTGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAAGCCAATCATTTTGCTGATTGATTTTGTGAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTgg                                                                               <  1:332854/141‑1 (MQ=255)                                                   tGCCAACTGTTTCGCCTTCCCTTGGTTGTACAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAAAAAAAAAACTGGTa                                                                             >  2:320775/1‑141 (MQ=255)                                                   tGCCAACTGTTTCGCCTTCCATTGTACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTGAAAAATAAAAAAACTGGTa                                                                             >  1:442969/1‑141 (MQ=255)                                                   tGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAACGGTa                                                                             >  2:566333/1‑141 (MQ=255)                                                     ccAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTAtt                                                                           >  1:591954/1‑141 (MQ=255)                                                        aCTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTcca                                                                        >  1:373966/1‑140 (MQ=255)                                                        aCTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATAGGATGATGAGATTTAAAAATAAACAAACTGGTATTACg                                                                        >  1:451600/1‑141 (MQ=255)                                                         ccgTTTCGCCTTCCATTGAACGCTCAATTTGCTTCTTAATCCAATCAGTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGa                                                                       <  1:527146/139‑1 (MQ=255)                                                          tGTTTCGCCTTCCATTTAACGGTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTATAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGaa                                                                      <  2:259540/141‑1 (MQ=255)                                                          tGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGaa                                                                      <  1:185944/141‑1 (MQ=255)                                                                gCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTtg                                                                <  1:33120/141‑1 (MQ=255)                                                                     ccATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGtat                                                           <  1:565838/141‑1 (MQ=255)                                                                     ccATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATATTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGtat                                                           >  1:540377/1‑141 (MQ=255)                                                                          gAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAAc                                                      <  2:519995/141‑1 (MQ=255)                                                                             cGCTCAATTTGCGTCTTAATCCAATCATTTTGCGGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTAAAAAACATa                                                   >  2:491425/1‑141 (MQ=255)                                                                               cTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAGAAAACTGGTATTCCGAATATTTGTGTATAAAACATAcc                                                 <  1:446965/141‑1 (MQ=255)                                                                                  aaTTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTg                                              <  1:27297/141‑1 (MQ=255)                                                                                        cGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATa                                        <  1:333791/141‑1 (MQ=255)                                                                                             tAATCCAATCATCTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAGAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAATATACCTTGAAAATAgatga                                   <  2:389970/141‑1 (MQ=255)                                                                                               aTCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGCAACTAGCTGata                                 >  2:542702/1‑141 (MQ=255)                                                                                                 ccAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATAtt                               <  2:382237/141‑1 (MQ=255)                                                                                                 ccAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATAtt                               <  2:43709/141‑1 (MQ=255)                                                                                                 acAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACAAAATAATATGATGATGAGAAATAAAAAAAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATAtt                               <  2:571374/140‑1 (MQ=255)                                                                                                  cAATCACTATGCTGATTGATTCTGTAAGCGAGCCGCGAACCAACAATAATACACAATCATACGACGATGAGAGTTAAAAATAAAAAAACACGCAAGCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATAttt                              >  2:336168/1‑141 (MQ=255)                                                                                                        ttttGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaaaa                        >  1:196640/1‑141 (MQ=255)                                                                                                         tttGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaaaaa                       >  1:627757/1‑141 (MQ=255)                                                                                                            gCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGCCTCAAGAAAAATTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACtt                    >  1:302844/1‑141 (MQ=255)                                                                                                             cTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACttt                   <  1:574807/141‑1 (MQ=255)                                                                                                             cTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACttt                   <  1:46762/141‑1 (MQ=255)                                                                                                              tgattgatTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTa                  >  1:585987/1‑141 (MQ=255)                                                                                                               gattgattTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACCAAAACTTTAt                 >  1:595764/1‑141 (MQ=255)                                                                                                                 ttgattTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTtctca               >  1:413774/1‑140 (MQ=255)                                                                                                                 ttgattTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTAtag               >  1:413839/1‑139 (MQ=255)                                                                                                                    attTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATg            >  1:583777/1‑141 (MQ=255)                                                                                                                    attTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGAGTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATg            >  1:462446/1‑141 (MQ=255)                                                                                                                      tttGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGaa          <  1:107884/141‑1 (MQ=255)                                                                                                                         gTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAg       >  2:212097/1‑141 (MQ=255)                                                                                                                            aGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGaaa    >  1:650353/1‑141 (MQ=255)                                                                                                                             gctaGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAAt   <  1:336168/138‑1 (MQ=255)                                                                                                                              cGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATg  >  1:174380/1‑141 (MQ=255)                                                                                                                                    |                                                                                                                                       ATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATG  >  USA300TCH1516_ALE/2027620‑2027885

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑