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%	39.0 / NA	15	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 (7/8);  total (7/8)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTA  >  USA300TCH1516_ALE/2010234‑2010480                                                                                                                                  |                                                                                                                      gtCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCa                                                                                                             >  1:51175/1‑140 (MQ=255)  tCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGACGATAAACATTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATTTAACCaa                                                                                                            >  1:44502/1‑140 (MQ=255)      ttttCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAatat                                                                                                        <  2:75066/140‑1 (MQ=255)               tCTTCCAAAGAAAACGTACACCGTTAAAATGCAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACACTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAcc                                                                                               <  1:214556/140‑1 (MQ=255)                      aaGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAAGCTAAAAAAATGTTAATTAACCCgctgaa                                                                                        >  2:206566/1‑135 (MQ=255)                                 cacCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGGAATCtt                                                                             >  1:187912/1‑140 (MQ=255)                                                 aatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatc                                                             <  1:285393/140‑1 (MQ=255)                                                    gggAAGATAAACAGTGCCGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCCATAATCATAGACTCATCGCCCTACTAAATAGGCATTAACTCGGATAAGATGAAATCTTTTGTTTGTTCAACAGCAtt                                                          <  2:145986/140‑1 (MQ=255)                                                       aaGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGACCATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAAt                                                       <  1:39141/140‑1 (MQ=255)                                                         gATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCGATAATAATTGTTATATAATCTAACCAAATATTCCTTAACCCGGTTAAAATGAAATCTTTTTTTTATTCAACATCATTAATCa                                                     >  1:265935/1‑140 (MQ=255)                                                            aaaCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCActc                                                  >  1:311027/1‑140 (MQ=255)                                                                          aaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGa                                    <  2:37309/140‑1 (MQ=255)                                                                                  ttCACATCTAAAAAGAACATTATGGAAAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTg                            <  2:245338/140‑1 (MQ=255)                                                                                     acaTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGatt                         >  1:184381/1‑140 (MQ=255)                                                                                                            tAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTa  <  2:51175/140‑1 (MQ=255)                                                                                                                                  |                                                                                                                      GTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTA  >  USA300TCH1516_ALE/2010234‑2010480

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: ‑