Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	9,280	G→A	13.4%	R750H (CGT→CAT)	gyrA →	DNA gyrase subunit A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	9,280	0	G	A	13.4%	134.2 / 10.2	52	R750H (CGT→CAT)	gyrA	DNA gyrase subunit A
Reads supporting (aligned to +/- strand):  ref base G (23/22);  new base A (5/2);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 4.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

CTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCAAAATGGTCGTGCAGCACAAGGTGTTCGCTTAATT  >  USA300TCH1516_ALE/9141‑9419                                                                                                                                             |                                                                                                                                            ggggATGTAGCTCATGCAAACAGTGTGGTTGAAGTATTAGGAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGAGTACCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCgt                                                                                                                                            <  2:204008/138‑1 (MQ=255)  ttGATGGAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTGAGCGTACGCCAGTGAATGACTATGGT‑TTATCCGATCGTGGTGGTAAAGGTATTATAACAGCTACGATTACTGAGGgta                                                                                                                                           <  1:402050/141‑1 (MQ=255)    gATGTAGGTAATGGAAAGAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCgtaat                                                                                                                                         <  2:176480/141‑1 (MQ=255)          gCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCgtaatggtaat                                                                                                                                   >  2:259256/1‑141 (MQ=255)              ttGCGAACAGGTTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAAtgttg                                                                                                                               <  2:327814/140‑1 (MQ=255)                 cAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTtgtat                                                                                                                            <  1:350338/141‑1 (MQ=255)                  aaaCAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCGGTTAATGACGATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTtgtatg                                                                                                                           >  1:302688/1‑141 (MQ=255)                  aaaCAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCATAATGGTAATGTtgtatg                                                                                                                           <  1:146055/141‑1 (MQ=255)                    aCAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCATCATGGCAATGTtgtatgta                                                                                                                         >  2:379169/1‑141 (MQ=255)                        tgtTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCAc                                                                                                                     <  1:83511/141‑1 (MQ=255)                                  gTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACt                                                                                                           <  1:283826/141‑1 (MQ=255)                                    aTTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGGGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCATAATGGTAATGTTGTCTGTATCACTAAAGTAACTgg                                                                                                         >  2:5418/1‑141 (MQ=255)                                    aTTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTAGCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTgg                                                                                                         <  2:222960/141‑1 (MQ=255)                                     ttAGGAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGt                                                                                                        <  1:145981/141‑1 (MQ=255)                                       agtagtTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAATGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTga                                                                                                      >  2:412031/1‑141 (MQ=255)                                              aCTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGAt                                                                                               <  1:184899/141‑1 (MQ=255)                                                 gagagtGGTTGTGATAAACGGACGCGAGGTAAAGACTAACGG‑ATATAAAAGAGGGGTGGTAAAGGTATTAATAAAGAGACGAGGACTGAGTGTAATGGTAATGTTGTATGTATCACTGTTGTAACTGGTGAAGAAGATTTa                                                                                            <  2:274438/136‑1 (MQ=255)                                                 gAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCATAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTa                                                                                            >  1:388582/1‑141 (MQ=255)                                                   aaaTGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAAt                                                                                          >  2:365192/1‑141 (MQ=255)                                                   aaaTGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTAATGCGCGCCGTGGGTATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAAt                                                                                          >  1:388417/1‑141 (MQ=255)                                                          tATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGtt                                                                                   <  2:261188/141‑1 (MQ=255)                                                          tATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGtt                                                                                   <  1:82810/141‑1 (MQ=255)                                                           ttGGTAAACGTAGGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTa                                                                                  <  2:314396/140‑1 (MQ=255)                                                           agggTAAACTTACGCGAATTAATGATTATCGC‑TTATCAAATCGGGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTa                                                                                  <  2:193546/139‑1 (MQ=255)                                                             ggTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACt                                                                                >  1:349379/1‑141 (MQ=255)                                                              gTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTa                                                                               >  1:99748/1‑141 (MQ=255)                                                              gTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTa                                                                               >  1:173436/1‑141 (MQ=255)                                                                  aCGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTCAATGGCGAAAAAGATTAAAGTATTGTTACTAATga                                                                           >  2:353860/1‑140 (MQ=255)                                                                    gTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAg                                                                         >  2:314920/1‑141 (MQ=255)                                                                      aCGCCAGTTAATGACTATCGCTTTATC‑AATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGgt                                                                       <  2:199820/141‑1 (MQ=255)                                                                      aCGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAATATTTAATGATTGTTACTAATGCAGgt                                                                       >  2:165587/1‑141 (MQ=255)                                                                         ccAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACACCTACTATTACTGTGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTc                                                                    <  1:367154/141‑1 (MQ=255)                                                                            gTTAATGACTTTCCC‑GGATCAAATCGCGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCatt                                                                 <  1:248414/141‑1 (MQ=255)                                                                                   aCTATCGC‑TTGCGAAAGCGTGGTGGTAAAGGTATTCAAATAGCTGCGATTACTGAGCAGAATGGTAATGTTGTATGTATCACTACAGTAACTGGTTAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGAc                                                          <  2:43354/141‑1 (MQ=255)                                                                                     tATCGC‑TTATCAGATCGGGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTa                                                        <  2:408042/141‑1 (MQ=255)                                                                                      aTCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAg                                                       >  1:326447/1‑141 (MQ=255)                                                                                         gC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATg                                                    >  1:359585/1‑141 (MQ=255)                                                                                         gC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATg                                                    >  2:309702/1‑141 (MQ=255)                                                                                               tCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCa                                               >  1:151258/1‑141 (MQ=255)                                                                                               tCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGAAATGTCGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCa                                               >  2:187539/1‑141 (MQ=255)                                                                                                taaaTCGTGGTGGGAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAGCTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTTTTTTGATTCGACTAGATGTTGCAg                                              <  2:382278/140‑1 (MQ=255)                                                                                                cAAATGGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTCACTGGTTAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAg                                              <  2:379961/141‑1 (MQ=255)                                                                                                   aTCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATCGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGata                                           >  2:89446/1‑141 (MQ=255)                                                                                                     cGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCATAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATAtt                                         >  2:304301/1‑141 (MQ=255)                                                                                                          tggtAAAGGTATGAAATGAGCAACGATTAATGAGAGTAATGGGAATGTTGTATGTATTATTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCa                                    <  2:123635/141‑1 (MQ=255)                                                                                                           gggaaaGGAATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCaa                                   <  2:4953/138‑1 (MQ=255)                                                                                                                        aaaCAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCAAAATGGTCGTgctg                      >  2:363522/1‑139 (MQ=255)                                                                                                                        aaaCAGCTACGATTACTGAGCATAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCAAAATGGTCGTgcag                      >  1:133185/1‑141 (MQ=255)                                                                                                                         aaCAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTCGCAGATATTTCTCAAAATGGTCGTtcagc                     >  2:346339/1‑141 (MQ=255)                                                                                                                                  gATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGCGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATACTTCTCAAAATGGTCGTGCAGCACAAGgtgt            <  1:284770/141‑1 (MQ=255)                                                                                                                                  gATTACAGAGCGCAATGGTAATGCTGAATGTATCACTACAGCATCAGGAGAAGAAAAGTTAATGATTGTTACTAATGCAGGTGGCATTGTTTGACTAGATGTTTCAGATACTTCTCAAAATGGTCATCCAGcacataacac            >  2:83545/1‑135 (MQ=255)                                                                                                                                    ttACTGAGCGTAATGGTAATGTTTTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCAAAATGGTAGTGCAGCACAAGATGTTc          >  2:129178/1‑141 (MQ=255)                                                                                                                                      aCTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCAAAATGGTCGTGCAGCACACGGCGTgcgc        >  2:351757/1‑141 (MQ=255)                                                                                                                                       cTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCAAAATGGTCGTGCAGCACACGGTGTTCGCt       >  1:121045/1‑141 (MQ=255)                                                                                                                                          aGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCAAAATGGTCGTGCAGCACAAGGTGTTCGCTTaa    <  1:6502/141‑1 (MQ=255)                                                                                                                                            cGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTAATAATGCAGGTGTCATTACTCGACTAATTGCTGCAGATATTTCTCAAAATGGTCGTGCAGCACAAGGTGTTCGCTTAAtt  >  1:282417/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                            CTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGC‑TTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCAAAATGGTCGTGCAGCACAAGGTGTTCGCTTAATT  >  USA300TCH1516_ALE/9141‑9419

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: ‑