Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,513,930	A→T	L413F (TTA→TTT)	USA300HOU_RS07375 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,513,930	0	A	T	100.0%	38.5 / NA	12	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (7/5);  total (7/5)

GCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATG‑TTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTA  >  USA300TCH1516_ALE/1513811‑1514024                                                                                                                         |                                                                                               gCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATG‑TTTTATTGTATTAGGATTATTAATg                                                                           <  2:77149/141‑1 (MQ=255)        tagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATG‑TTTTATTGTATTAGGATTATTAATGCCattat                                                                    <  1:209654/141‑1 (MQ=255)        tagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATG‑TTTTATTGTATTAGGATTATTAATGCCattat                                                                    <  2:166912/141‑1 (MQ=255)        tagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGAGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATG‑TTTTATTGTATTAGGATTATTAATGCCattat                                                                    <  2:247846/141‑1 (MQ=255)          gtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATG‑TTTTATTGTATTAGGATTATTAATGCCATTAttt                                                                  >  2:167261/1‑141 (MQ=255)                   ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATG‑TTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                         >  1:217831/1‑141 (MQ=255)                         gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAACACAACCGAATCTCTATCACTCCTAAACTGATTTTACT‑AACTAGTATTATTAATGCAATTATTTGGATTATCACTTATc                                                   >  1:186441/1‑141 (MQ=255)                         gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATG‑TTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATc                                                   <  1:175321/141‑1 (MQ=255)                                                                     aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATG‑TTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtcg       >  2:168279/1‑141 (MQ=255)                                                                     aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATG‑TTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtcg       >  2:92243/1‑141 (MQ=255)                                                                       tACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAAGATG‑TTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTg     >  1:247024/1‑141 (MQ=255)                                                                          cacaTCGCGTAAAAAAACCAGCATCTATATCACTCATATTATG‑TTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTa  >  1:152319/1‑141 (MQ=255)                                                                                                                         |                                                                                               GCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATG‑TTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTA  >  USA300TCH1516_ALE/1513811‑1514024

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: ‑