Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,010,363	C→T	100%	C146Y (TGT→TAT)	USA300HOU_RS10125 ←	Putative multidrug export ATP‑binding/permease protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,010,363	0	C	T	100.0%	55.4 / NA	20	C146Y (TGT→TAT)	USA300HOU_RS10125	Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (9/11);  total (9/11)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTT  >  USA300TCH1516_ALE/2010227‑2010486                                                                                                                                         |                                                                                                                            ttCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAAt                                                                                                                          <  2:285559/140‑1 (MQ=255)       tgtCAATTTTCTTAAACTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACACCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAAcc                                                                                                                    <  2:155960/140‑1 (MQ=255)               ttCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTc                                                                                                            <  1:194228/140‑1 (MQ=255)                  ttAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAtt                                                                                                         >  2:85575/1‑140 (MQ=255)                             aaGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTACAATAATAAATGTTATATAATCTAACCAAATATTCATTAACCCGGTTaa                                                                                              >  1:217899/1‑140 (MQ=255)                                        cacCGTTAAAATGGTAAGTGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCtt                                                                                   <  2:45277/140‑1 (MQ=255)                                                  atgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTc                                                                         <  2:262175/140‑1 (MQ=255)                                                    gtaaaatgGGAAGATAAAAAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGATATATAATCTAACCAAATATTCATTATCCCGGTTAAAATGAAATCTTTTGTTTGTTCaa                                                                       <  2:32868/140‑1 (MQ=255)                                                         atgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatca                                                                  <  2:223579/140‑1 (MQ=255)                                                                gATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAAACAAATATTCATTAACACGGTTAAAATGAAATATTTTGTTTGTTCAACATCATTAATCa                                                           >  1:240230/1‑140 (MQ=255)                                                                               tAAAGTCATGTTCACATCTAAAAAAAACATTTTCGAGAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACtt                                            <  1:53751/140‑1 (MQ=255)                                                                                      aaTTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTAc                                     <  2:283972/140‑1 (MQ=255)                                                                                         ttCACATCAAAATAGGACAGTATGGATAGTGCAATAATAATTGTTATATTATCTTACCAAATATTCATTAACCCGGCTAAAATGAATTCTTTGGTTTGTTTGTCATCATTAATCACTCTAGATATTACTTGACCTACTTg                                  <  2:167036/140‑1 (MQ=255)                                                                                          tCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGa                                 >  1:33075/1‑140 (MQ=255)                                                                                                 tAAAAAGAACATTATGGATAGTGCAATACTAATTGATATCTAATCTAACCAAATATTCATAAACCCGGTTAAAATGAAATATTTTGTTTGTTCAAAATCATTAATCACTCTAGATATTACTTGACCACGTTGATTATAAg                          >  2:2276/1‑140 (MQ=255)                                                                                                         aCATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCATATGTTTGTACAACATCATTAATCACACTAGATATTACTATACCTACTGGAGTATTAGCATAAAAt                  >  1:96885/1‑140 (MQ=255)                                                                                                          cATTAGGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtc                 <  2:64199/140‑1 (MQ=255)                                                                                                             tATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGCCCTCCTTGATTATTAGCATAAAAtctcc              >  2:209572/1‑139 (MQ=255)                                                                                                                    aGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTaa       >  1:271779/1‑140 (MQ=255)                                                                                                                         aataataatTGTTATATAATCTAACCAAATATTCATTAACACGTACAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGAAATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCtt  >  1:153531/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                            TTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTT  >  USA300TCH1516_ALE/2010227‑2010486

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: ‑