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%	27.5 / NA	12	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (8/4);  total (8/4)

TTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  USA300TCH1516_ALE/1513814‑1514065                                                                                                                     |                                                                                                                                        ttagtaGTAGCCATTGTCATGGGGTTTGTCTATTGGATAAAGCGTAAAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                                  <  2:11194/140‑1 (MQ=255)     tagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTATTGCTatta                                                                                                              >  2:113726/1‑140 (MQ=255)         agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                          >  2:188767/1‑140 (MQ=255)         agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATACCATTATTTg                                                                                                          >  1:150993/1‑140 (MQ=255)                    tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTATGATTATTAATAACATTAATTGGATTATCACtt                                                                                               >  1:2596/1‑140 (MQ=255)                                        aaGCGTACAAAAAATACTGCAATAAAAGTTCTACATCGCGTAAAAAAACCAGCATCTATATTTCTTATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATCTATAATTGa                                                                           <  1:15214/140‑1 (MQ=255)                                               cAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAata                                                                    <  2:213181/140‑1 (MQ=255)                                                         tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTCTATCACTCATAATATGTTTTATTGTATTAAGATTATTAATACAATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                          >  1:124502/1‑140 (MQ=255)                                                                  aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTTTATTTATAATTGAATTAATATTATATATTAAATAtcttc                                                 >  2:241626/1‑140 (MQ=255)                                                                       cacaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCt                                            >  1:20353/1‑140 (MQ=255)                                                                                          aGCATCTATATCACTCATAATATGTTTTATTTTATTAGGATTATTAATGCCATTATTTGGATCATTACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAATCAATAATGCACTTaaa                         <  2:225625/140‑1 (MQ=255)                                                                                                                 gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGACATTTACa  >  1:130835/1‑140 (MQ=255)                                                                                                                     |                                                                                                                                        TTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  USA300TCH1516_ALE/1513814‑1514065

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑