Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	874,718	A→C	100%	K541N (AAA→AAC)	clfA →	Clumping factor A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	874,718	0	A	C	100.0%	112.1 / NA	38	K541N (AAA→AAC)	clfA	Clumping factor A
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (26/12);  total (26/12)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AATAGCAAAGGTGATTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAAACCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCTA  >  USA300TCH1516_ALE/874587‑874851                                                                                                                                    |                                                                                                                                       aaTAGCAAATGTGATTTAGCTTTACGTTCAACTATATATGGGTATAGCCCAAAAACAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAgttgt                                                                                                                                <  1:360618/140‑1 (MQ=255)    aGCAAAGGTGATTTCGCTTTACGTTCAACTTTATATGGGTCTCACTCGTATATAATTTGGCGCTATATGTCATGGGACAACGAAGTAGCATGTAATCACGGATCAGGTTCTGGTGACGGTATCGATCACCCAgttgttgc                                                                                                                             >  1:3296/1‑138 (MQ=255)       aaaGGTGATTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGa                                                                                                                          >  1:635734/1‑140 (MQ=255)        aaGGTGATTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCAAAAACCAAGTTGTTCCTaaa                                                                                                                         >  1:321588/1‑140 (MQ=255)        aaGGTGATTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGATGACGGTATCGATAACCCAGTTGTTCCTGaa                                                                                                                         >  1:226538/1‑140 (MQ=255)                             cAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGaa                                                                                                   >  1:274396/1‑140 (MQ=255)                                    atatGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATGGAAc                                                                                            >  1:200332/1‑140 (MQ=255)                                    atatGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGAATCGATAACCCAGTTGTTCCTGAACAACCTGATGCGC‑CTGGTGACATTGAAc                                                                                            >  1:640462/1‑140 (MQ=255)                                    atatGGGTATAACTCGAATATAATTTGGCGCTCTATGTAATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGCTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAAc                                                                                            >  1:425648/1‑140 (MQ=255)                                    atatGGGTATAACTCGAATATAATTTGGCGCTCTATGTAAAAGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAAc                                                                                            >  1:336149/1‑140 (MQ=255)                                     tatGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAAcc                                                                                           <  1:503576/140‑1 (MQ=255)                                      atGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAAcaa                                                                                          >  1:273880/1‑138 (MQ=255)                                               aCTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCagag                                                                                 >  1:722885/1‑140 (MQ=255)                                                 tCGAATATAATTTGGCGCTCTATGTCATTAGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGa                                                                               <  1:750455/140‑1 (MQ=255)                                                 tCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGa                                                                               >  1:577446/1‑140 (MQ=255)                                                 tCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTAGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACTAATTCCAGGGGa                                                                               >  1:69394/1‑140 (MQ=255)                                                 tCGAATATAATTTGGCGCTCTATGCCATCCAGCGACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGATC‑CTGGTGAAATTGAACCAATTCCAAAGGa                                                                               >  1:369730/1‑140 (MQ=255)                                                  cGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGA‑CTGGTGAAATTGAACCAATTCCAGAGGAt                                                                              >  1:725707/1‑140 (MQ=255)                                                   gAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATTACGAATCAGGTTCTGGTGACGGTATCGATAACCCAGTTATTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTGCACAGGAtt                                                                             >  1:296546/1‑140 (MQ=255)                                                       ataATTTGGCGCTCTATGTCATGGGATAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGa                                                                         <  1:123837/140‑1 (MQ=255)                                                                               gACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACTCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTgg                                                 <  1:37588/140‑1 (MQ=255)                                                                               gACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATACTGACCCAGGTTCAGATTCTgg                                                 >  1:671419/1‑140 (MQ=255)                                                                                  aaCGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCGAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAg                                              >  1:99558/1‑140 (MQ=255)                                                                                   aCGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGTCAACCGCTAG‑CAACTTGAACCAATACCAAAGGATTAAGATACTGACCCAGAATAAAATTCTGGAAGc                                             >  1:364201/1‑140 (MQ=255)                                                                                      aaGTAGCATTTAATAACGGATCAGGTTCTGGTGATGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAAATGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGAt                                          <  1:73261/140‑1 (MQ=255)                                                                                       aGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGCTTCAGATTCTGACCCAGGTTCAGATCCTGGCAGCGGtt                                         >  1:225996/1‑140 (MQ=255)                                                                                           gCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCAAGAGGAATCAGATTCTGACCGAGGTTCAGATTCTGGCAACGATTCTaa                                     >  1:108732/1‑140 (MQ=255)                                                                                                 aataaCGGTTCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGa                               <  1:120560/140‑1 (MQ=255)                                                                                                 aataaCGGATCAGGTTCTGGTGACGTTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGa                               <  1:337356/140‑1 (MQ=255)                                                                                                 aataaCGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGa                               >  1:433210/1‑140 (MQ=255)                                                                                                    aaCGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACGCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAg                            <  1:357353/140‑1 (MQ=255)                                                                                                         aTCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGtt                       <  1:91467/140‑1 (MQ=255)                                                                                                           cAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCAAGGTTCAGATTCTGGAAGCGATTCTAATTCAGATGGCGGTTCa                     >  1:606852/1‑140 (MQ=255)                                                                                                              gTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTCACCCAGGTTCAGATTCTGGCCGCGATTCTAATTTAGATAGCGTTTTAGAt                  >  1:734766/1‑140 (MQ=255)                                                                                                                 cTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCg               >  1:375748/1‑140 (MQ=255)                                                                                                                            aTCGATAACCCAGTTGTTACTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGAGAGCGGTTCAGATTCGGGTAGTGATTc    <  1:667642/140‑1 (MQ=255)                                                                                                                             tCGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATCCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCt   <  1:720652/140‑1 (MQ=255)                                                                                                                              cGATAACCCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATACCAGAGGATTCAGATTCTGACCCAGGTACAGAATCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCTa  >  1:610518/1‑140 (MQ=255)                                                                                                                                    |                                                                                                                                       AATAGCAAAGGTGATTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAAACCAGTTGTTCCTGAACAACCTGATGAGC‑CTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCTA  >  USA300TCH1516_ALE/874587‑874851

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑