Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,027,751	C→G	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	98.4%	189.2 / NA	61	V66L (GTA→CTA)	vraS	Sensor protein VraS
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base G (41/19);  minor base A (1/0);  total (42/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAG  >  USA300TCH1516_ALE/2027617‑2027888                                                                                                                                       |                                                                                                                                          tgtattgtatAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAAcc                                                                                                                                     <  2:640540/141‑1 (MQ=255) tgtATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAAcc                                                                                                                                     <  2:223422/141‑1 (MQ=255) tgtATGGTATAAATCTAACGTTTCACCATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAAcc                                                                                                                                     <  1:610699/141‑1 (MQ=255)    aTGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACcaac                                                                                                                                  <  1:16695/141‑1 (MQ=255)    aTGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACcaac                                                                                                                                  <  1:740705/141‑1 (MQ=255)               cTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATAcaca                                                                                                                       <  2:810723/141‑1 (MQ=255)                 aaCGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACaat                                                                                                                     <  1:77664/141‑1 (MQ=255)                    gTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGAGTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACaataat                                                                                                                  >  2:509949/1‑141 (MQ=255)                      tccACTATACATCTTTATATCTTTGTCATTAATGCTAACTGTTTCGCCTTACATTGAACGCTCAACTTGCGTCTTAATCCAATCATGTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAatat                                                                                                                <  2:130806/139‑1 (MQ=255)                       tCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATatg                                                                                                               >  1:441313/1‑141 (MQ=255)                       tCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTAAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATatg                                                                                                               >  1:249009/1‑141 (MQ=255)                        cACTATATATTTCTATATTTTGATCATTATTGGCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGTTTGATTTTGTAAGCGAGAGACGAACCAACAATAATACACAAAAatataa                                                                                                              >  1:236978/1‑139 (MQ=255)                         aCTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATATAGTAAGCGAGTAGCGAACCAACAATAATACACAATAATatgag                                                                                                             >  1:428542/1‑140 (MQ=255)                                atTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATgaga                                                                                                      <  1:958726/141‑1 (MQ=255)                                         ttttGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaaa                                                                                             >  2:589804/1‑140 (MQ=255)                                           ttGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaataa                                                                                           >  2:34122/1‑141 (MQ=255)                                           ttGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaataa                                                                                           >  2:818445/1‑141 (MQ=255)                                            tGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaataaa                                                                                          >  2:864747/1‑141 (MQ=255)                                             gATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACGAACAATAATACACAATAATATGATGATGAGATTtaaaaataaaa                                                                                         >  2:509368/1‑141 (MQ=255)                                             gATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaataaaa                                                                                         >  2:89661/1‑141 (MQ=255)                                                   tAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACCCAATAATATGATGATGAGATTTAAAAATACAAAAACTg                                                                                   >  2:60302/1‑141 (MQ=255)                                                      tGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAAGAATACACAATAATATGATGATGAGCTTTAAAAATAAAAAAACTGGTa                                                                                >  1:762558/1‑141 (MQ=255)                                                       gCCAACTGTTTCTCCTTCCATTAAACGCTCAATTTGCGTCTTAGTCCAATCATTTTGCTGGTTGATTTTATAACCGAGTAGCGAACCAACAATAATACACAATAATACAATGATTAGATTTATAAAAAAAAAGACAGGAAt                                                                               >  2:351469/1‑141 (MQ=255)                                                          aaCTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAAATTTAAAAATAAAAAAACTGGATTTcc                                                                            >  2:385547/1‑141 (MQ=255)                                                           aCTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGCACCAACAATCATACACAATACTATAATGATGAGATTTAAAAATAAAAAAACTGTGATTCCg                                                                           >  2:207317/1‑141 (MQ=255)                                                           aCTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGACTAATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATTATGAGATTTAAAACTAAAAAAACTGGGATTCCg                                                                           >  2:355297/1‑141 (MQ=255)                                                             tGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCTaa                                                                         >  2:311279/1‑141 (MQ=255)                                                              gTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAat                                                                        >  2:854820/1‑141 (MQ=255)                                                              gTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAat                                                                        >  2:147391/1‑141 (MQ=255)                                                               tttCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGAATTCCGAata                                                                       >  1:548172/1‑141 (MQ=255)                                                                  cGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATAttt                                                                    >  1:197170/1‑141 (MQ=255)                                                                  cGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATAttt                                                                    >  1:223400/1‑141 (MQ=255)                                                                  cGCCTTCAATTGAACGCTCAATTTGCGTCTTAGGCCAAGCATTTTGACAATTGATTTTACAACCGATTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACAGGAATTCCGAATAttt                                                                    >  2:701695/1‑141 (MQ=255)                                                                    ccTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGTTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACGCTATAATATGATGATGAGATTGAAAAATAAAAAAACTGGTATTCCGAATATTtgt                                                                  >  2:544701/1‑141 (MQ=255)                                                                    ccTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTtgt                                                                  >  2:842695/1‑141 (MQ=255)                                                                    ccTTCCATTGAACGCTCAATTTGCGTCTTAATACAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAAACAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATAttttt                                                                  >  2:477592/1‑139 (MQ=255)                                                                       tcgaTTGAACGCTCAATTTGCGTCTTAATCCAATCCTTTTGCTGATTGCGTTTGTAAGCGAATCGCGCACCACCAATAACACACACAAATATGATACTGAGATTTAAAAATAAAAAAACTGGTATTACGAATATTGGTGta                                                               >  2:481352/4‑141 (MQ=255)                                                                               aCGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATCTTTGTGTATAAAACAt                                                       <  1:493021/141‑1 (MQ=255)                                                                               aCGCTCAATTTGCGTCTTAAACCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAAAAAAAAAAAAAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACAt                                                       <  1:58021/141‑1 (MQ=255)                                                                                    cAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACCATAATACACAATAATATGATTATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCtt                                                  <  1:197746/141‑1 (MQ=255)                                                                                    cAATCTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCtt                                                  <  1:711796/141‑1 (MQ=255)                                                                                           cGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGGGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATa                                           <  2:428542/141‑1 (MQ=255)                                                                                                        tccttttGCTGATTGATTTTGTAAGCTAGTAGCGAACCAACGATAATACACAATAATATGATGATGAGATTTAAAAATAAAATAACTGCTATTCCGGATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACa                              <  1:605813/138‑1 (MQ=255)                                                                                                        tCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACa                              <  1:631118/141‑1 (MQ=255)                                                                                                          aTTTTGCTGATTGATTTTGTAAGCGAATAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTATGTATAAAACATACCTTAAAAATAGAAGATATATTCaaa                            >  2:269393/1‑141 (MQ=255)                                                                                                           ttttGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaaaa                           >  2:489113/1‑141 (MQ=255)                                                                                                             ttGCTGATAGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATATTATGATGATGAGATTTAAAAATAAAAAAACTGGTAATCCGAATATTTGTGTATAAAACAGACCTTGAAAATAGATGATATTTACAAAAAc                         >  2:733334/1‑141 (MQ=255)                                                                                                               gCTGATTGATTTTGTAAGCGAGTAGCGACCCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGGGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACtt                       >  1:640931/1‑141 (MQ=255)                                                                                                               gCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACtt                       >  2:778449/1‑141 (MQ=255)                                                                                                                 tgattgatTTTGTAAGCGAGTCGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACtttt                     >  1:516821/1‑140 (MQ=255)                                                                                                                 tgattgatTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTCCAAAACCTCTa                     >  2:828682/1‑141 (MQ=255)                                                                                                                    ttgattTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCg                  >  1:540220/1‑141 (MQ=255)                                                                                                                           tGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACa           >  1:349182/1‑141 (MQ=255)                                                                                                                           tGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACa           >  1:349219/1‑141 (MQ=255)                                                                                                                            gTAAGCGAGTCGCGAACCAACAATAATACACAACAAACTGATGTTGGGATTTAAAAATAACAAAACTGGAATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATAGATGAACaa          >  2:408743/1‑140 (MQ=255)                                                                                                                            gTAAGCGAGTAGCGAACCAACAATAATACACAGTAATATGATAATAAGATTTAAAAATAAAAAAACTTGTATTCCGAATATTTGTGTATAAAAAATACCTTGAAAATAGATGATATTTAAAAAAACTTTATCAATGAACAg          >  2:407269/1‑141 (MQ=255)                                                                                                                            gTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAAAAg          >  2:46019/1‑141 (MQ=255)                                                                                                                              aaGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATGGATGAAAAGaa        >  1:274630/1‑141 (MQ=255)                                                                                                                               aGCGAGTAGCGAAACAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGaaa       <  1:129292/141‑1 (MQ=255)                                                                                                                               aGCGAGGAGAGAACTAACAAGAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACGCGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGaca       <  2:659464/141‑3 (MQ=255)                                                                                                                                    gTAGCGAACCAACAATAATACACAATAATATGATGATGAGATATAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAg  <  2:598809/141‑1 (MQ=255)                                                                                                                                       |                                                                                                                                          TGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAG  >  USA300TCH1516_ALE/2027617‑2027888

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑