Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,010,363	C→T	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%	73.2 / NA	25	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 (17/8);  total (17/8)

TTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTT  >  USA300TCH1516_ALE/2010227‑2010496                                                                                                                                         |                                                                                                                                      ttCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATc                                                                                                                                   >  1:19229/1‑141 (MQ=255)         tCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCaaa                                                                                                                           >  2:38149/1‑141 (MQ=255)                tCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTAAt                                                                                                                    >  2:151029/1‑141 (MQ=255)                     tggttCCAAAGAAAATGGACAGCGGTAGAATGTAAGATGTGAAGATAAACAGTGCTGCTAAAGTCAATGTCACATCTAAAAAGAACATTATGGATAAGGAGCGAATAGTTGTTATATACTCTAACCAAATATTCATTAAcc                                                                                                               <  2:129178/138‑1 (MQ=255)                          ccAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATACTAATTGTTATCTACTCTAACCAAATATTCATTAACCCGGtt                                                                                                          >  1:28545/1‑141 (MQ=255)                          ccAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGtt                                                                                                          >  1:39680/1‑141 (MQ=255)                          ccAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACACGGtt                                                                                                          >  1:33601/1‑141 (MQ=255)                                aaaaCGTACACCTTTAAAATGTAAAAGGGAAGGATAAACAGGGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATg                                                                                                    <  2:122967/141‑1 (MQ=255)                                              aaaaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgtttg                                                                                      <  2:146564/140‑1 (MQ=255)                                               aaaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCACTCTATGTTCTAAAAATAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTttgtttgt                                                                                     <  2:127292/141‑1 (MQ=255)                                               aaaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATCGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATCACCCCGGCTAACATGAACTCTTttgtttgt                                                                                     >  1:60440/1‑141 (MQ=255)                                               aaaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTttgtttgt                                                                                     <  2:127677/141‑1 (MQ=255)                                                        aatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACTACAGATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatca                                                                            >  1:234741/1‑141 (MQ=255)                                                                 aTAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCAct                                                                   >  1:224986/1‑141 (MQ=255)                                                                                agaatCAATTTCACATCTAAAAAGAACATAACGGATAGTGCAATAATAATTGTTATATAATCTAACCACATATTCATTAACCCAGTAAAAATAAAATATTTTGTTTATTCACAAACATTAATCACACTAAATACTACttca                                                    >  2:69401/5‑139 (MQ=255)                                                                                     cAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTAc                                               >  1:269210/1‑141 (MQ=255)                                                                                              aTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGattatt                                      <  1:69239/141‑1 (MQ=255)                                                                                                cTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTCCTTGATTATTAg                                    >  1:110130/1‑141 (MQ=255)                                                                                                cTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAg                                    >  1:41826/1‑141 (MQ=255)                                                                                                  aaaaaGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCa                                  <  2:224986/141‑1 (MQ=255)                                                                                                          cATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACATACTTGATTATTAGCATAAAAtct                          >  1:255414/1‑141 (MQ=255)                                                                                                             tATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTCAAAATGAAATCTTTTGTTTGTGCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGc                       <  1:92703/141‑1 (MQ=255)                                                                                                                               aatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATg     >  1:240290/1‑141 (MQ=255)                                                                                                                                 ttGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGt   >  1:209127/1‑141 (MQ=255)                                                                                                                                  tGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAGTGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGtt  >  2:145542/1‑141 (MQ=255)                                                                                                                                         |                                                                                                                                      TTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTT  >  USA300TCH1516_ALE/2010227‑2010496

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: ‑