Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	874,718	A→C	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%	72.0 / NA	19	K541N (AAA→AAC)	clfA	Clumping factor A
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (13/6);  total (13/6)

ATAGCAAAGGTGATTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAAACCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCTACATCAG  >  USA300TCH1516_ALE/874588‑874857                                                                                                                                   |                                                                                                                                            aTAGCAAAGGTGATTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAAAATACTTTGGCAAAATATGTCCTGGCACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGaacaa                                                                                                                           <  1:238127/149‑1 (MQ=255)                           tCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAAcc                                                                                                 >  1:307398/1‑149 (MQ=255)                                   atatGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCag                                                                                         <  1:78867/149‑1 (MQ=255)                                      tGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAgg                                                                                      >  1:15583/1‑149 (MQ=255)                                             aaCTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGa                                                                               >  1:124027/1‑149 (MQ=255)                                             aaCTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGa                                                                               >  1:148934/1‑149 (MQ=255)                                                     tataATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGAcc                                                                       >  1:90554/1‑149 (MQ=255)                                                              gcgcTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAg                                                              <  1:29705/149‑1 (MQ=255)                                                                        tCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTCACCCAGGTTCAGATTCTGGCAg                                                    >  1:227697/1‑149 (MQ=255)                                                                         cATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGc                                                   >  1:74590/1‑149 (MQ=255)                                                                                             tttAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCgg                               >  1:217229/1‑149 (MQ=255)                                                                                               taataaCGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGtt                             <  1:176888/149‑1 (MQ=255)                                                                                                 ataaCGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCa                           >  1:307582/1‑149 (MQ=255)                                                                                                          cAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGt                  <  1:243516/149‑1 (MQ=255)                                                                                                                  ggTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTc          <  1:337972/149‑1 (MQ=255)                                                                                                                  ggTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTc          >  1:130793/1‑149 (MQ=255)                                                                                                                         gTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCTACATCa   >  1:23975/1‑149 (MQ=255)                                                                                                                         gTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCAGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCTACAtaa   >  1:120277/1‑147 (MQ=255)                                                                                                                          tATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATGCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCTACATCAg  >  1:67141/1‑149 (MQ=255)                                                                                                                                   |                                                                                                                                            ATAGCAAAGGTGATTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAAACCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCTACATCAG  >  USA300TCH1516_ALE/874588‑874857

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