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%	63.8 / NA	21	K541N (AAA→AAC)	clfA	Clumping factor A
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (12/9);  total (12/9)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGCAAAGGTGATTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAAACCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCTACAT  >  USA300TCH1516_ALE/874590‑874854                                                                                                                                 |                                                                                                                                         aGCAAAGGTGATTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACAGATCAGGCTCGGGTGACGGTATCGATAACCCAGTTGTTCCt                                                                                                                              >  1:247214/1‑141 (MQ=255)   cAAAGGTGACTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGCAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTcagga                                                                                                                            <  1:250761/141‑5 (MQ=255)                                   atGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAAAAACGGATCAGGTTCTGGGGACGGTATCGATAACCCAGTTGTTCCTAAACAACCTGATGAGACTGGTGGAAATGAACCaa                                                                                            >  1:56664/1‑141 (MQ=255)                                    tGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCGGAGGGGCCTCGTGCAAACGAAGCAAt                                                                                           >  1:559799/1‑141 (MQ=255)                                     gggTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGAGCACTCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGCAATTTAACCAAtt                                                                                          >  1:159842/1‑141 (MQ=255)                                                      aaTTTGGCGCTCTAGGTCATGGGACAACGAAGTAGCATTTAATAAAGGAGCAGGAGCGGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTc                                                                         <  1:445289/141‑1 (MQ=255)                                                                               aaCGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGc                                                >  1:518562/1‑141 (MQ=255)                                                                                 cGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCcgcgg                                              >  1:145487/1‑140 (MQ=255)                                                                                    aGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTc                                           <  1:238619/141‑1 (MQ=255)                                                                                       aGCATTTAATAACGTATCAGGTGCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTaa                                        <  1:182740/141‑1 (MQ=255)                                                                                               ataaCGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATa                                >  1:164992/1‑141 (MQ=255)                                                                                                 aaCGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGc                              >  1:32661/1‑141 (MQ=255)                                                                                                  aCGGATCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGATCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCg                             >  1:352236/1‑141 (MQ=255)                                                                                                     gaccAGGTTCTGGTGACGGTATCGATAACCCAGCTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGtt                          <  1:100272/138‑1 (MQ=255)                                                                                                       tCAGGTTCTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAGGTCAGATAGTGGTGCa                        >  1:129980/1‑141 (MQ=255)                                                                                                              cTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACGTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCGGCGATTCTAATTCAGATAGCGGTTTAGagtaag                 >  1:10409/1‑136 (MQ=255)                                                                                                              cTGGTGACGGTATCGATAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCCGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGCTTCgg                 >  1:132622/1‑141 (MQ=255)                                                                                                                        taccgctAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTc       <  1:37712/135‑1 (MQ=255)                                                                                                                        tATCGATACCCCAGTTGTTCGTGAACAACCTGCGGGGCCCGGAGGGTTCGAGCCAATTCTAGAGGATTCATATTCGGGCCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTc       <  1:271892/141‑1 (MQ=255)                                                                                                                        tATCGATAACCCAGTTGTTCCGGAACAACCTCATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTc       <  1:37696/141‑1 (MQ=255)                                                                                                                             aTAACCCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCTACAt  <  1:514924/141‑1 (MQ=255)                                                                                                                                 |                                                                                                                                         AGCAAAGGTGATTTAGCTTTACGTTCAACTTTATATGGGTATAACTCGAATATAATTTGGCGCTCTATGTCATGGGACAACGAAGTAGCATTTAATAACGGATCAGGTTCTGGTGACGGTATCGATAAACCAGTTGTTCCTGAACAACCTGATGAGCCTGGTGAAATTGAACCAATTCCAGAGGATTCAGATTCTGACCCAGGTTCAGATTCTGGCAGCGATTCTAATTCAGATAGCGGTTCAGATTCGGGTAGTGATTCTACAT  >  USA300TCH1516_ALE/874590‑874854

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: ‑