Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,188,185	C→T	R140C (CGC→TGC)	pbpB →	Penicillin‑binding protein 2B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,188,185	0	C	T	100.0%	84.3 / NA	26	R140C (CGC→TGC)	pbpB	Penicillin‑binding protein 2B
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (18/8);  total (18/8)

AAGGCGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGACGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTAATTGGTAGAGCTCAGAAAAATC  >  USA300TCH1516_ALE/1188041‑1188329                                                                                                                                                 |                                                                                                                                                 aaGGCGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCaa                                                                                                                                              >  2:277614/1‑149 (MQ=255)    gCGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAgg                                                                                                                                           >  1:207348/1‑149 (MQ=255)    gCGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATATACAGTCATTAATATGAAGCAAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGAAAAgg                                                                                                                                           >  1:97152/1‑149 (MQ=255)     cGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGa                                                                                                                                          >  1:243408/1‑149 (MQ=255)      gAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGaa                                                                                                                                         >  1:117448/1‑149 (MQ=255)                  tAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGt                                                                                                                             >  2:14617/1‑149 (MQ=255)                  tAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGt                                                                                                                             >  2:14606/1‑149 (MQ=255)                  tAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGt                                                                                                                             >  1:244839/1‑149 (MQ=255)                     aaaaCCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATc                                                                                                                          >  2:261223/1‑149 (MQ=255)                        aCCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAgg                                                                                                                       <  1:65324/149‑1 (MQ=255)                        aCCTAGGCATGTAGTTAATAAAAAAGAGACTGAAAAGAAATTATCTACAGTAATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAgg                                                                                                                       <  1:33916/149‑1 (MQ=255)                            aGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACaa                                                                                                                   <  2:59667/149‑1 (MQ=255)                                       agATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATGGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATag                                                                                                        <  2:60648/148‑1 (MQ=255)                                                         aaaGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTg                                                                                      <  1:213496/149‑1 (MQ=255)                                                         aaaGAAATTATCTACAGTCATTAACATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTg                                                                                      <  2:214997/149‑1 (MQ=255)                                                                    cTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTa                                                                           >  2:49556/1‑149 (MQ=255)                                                                     tACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTACAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTGTttatttat                                                                          >  2:60244/1‑149 (MQ=255)                                                                                    gAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAAc                                                           >  1:137486/1‑149 (MQ=255)                                                                                     aaGCCAGAGCAAACTGAAAATAGACTTAGTTAAAAGAAAGCCTTCCAATTTGAATTTTGATGCAAAGGTACAAATTTAACGTATCAGTACAAATTGAAAATAGAGAAAATGAATTTGCCTGCTACTTCTTTATTGCCTGAAACAGAACg                                                          >  2:30275/1‑149 (MQ=255)                                                                                               aaaTTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCa                                                >  1:237993/1‑149 (MQ=255)                                                                                                                     aaagaaagCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACt                          <  1:3035/149‑1 (MQ=255)                                                                                                                        gaaagCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTaa                       >  1:71234/1‑149 (MQ=255)                                                                                                                        gaaagCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTaa                       >  1:277503/1‑149 (MQ=255)                                                                                                                            gCTTTCCAAATTGAATTTGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTAATTgg                   >  2:124899/1‑149 (MQ=255)                                                                                                                             cTTTCCAAATTGAATTTGGTTGCAAAGCACCAAAAATAACGTCTCAGGACAACTTGTAAATAAAGAAAATGAATATGCCTGGTATTTCTTTATTACCGGAAACAAAACGCTTTTATCCAAATGGCAATTTAGCATCATACTTAATTGGt                  >  2:27979/1‑149 (MQ=255)                                                                                                                                             tGGATGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTAATTGGTAGAGCTCAGAAAAATc  <  2:117448/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                 AAGGCGAGTGCCAATTCTAAAAAACCTAGGCATGTAGTTGATAAAAAAGAGACTGCAAAGAAATTATCTACAGTCATTAATATGAAGCCAGAGGAAATTGAAAAGAGACTTAGTCAAAAGAAAGCTTTCCAAATTGAATTTGGACGCAAAGGAACAAATTTAACGTATCAGGACAAATTGAAAATAGAGAAAATGAATTTGCCTGGTATTTCTTTATTGCCTGAAACAGAACGCTTTTATCCAAATGGCAATTTTGCATCACACTTAATTGGTAGAGCTCAGAAAAATC  >  USA300TCH1516_ALE/1188041‑1188329

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑