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%	41.0 / NA	16	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (10/6);  total (10/6)

ATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTT  >  USA300TCH1516_ALE/1513798‑1514047                                                                                                                                     |                                                                                                                      atttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGTATAAAGCGTACAAAAAATCCTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATTTTTTAATGtttt                                                                                                               >  2:239075/1‑141 (MQ=255)                               tGGCATGGGGCTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCCCGTAAAAAAACCAGCATCTATATCACTCATAATATATCTTATTGTATTAGAATTATTAATGCCATTATTTGGATAAtt                                                                                 >  2:57211/1‑140 (MQ=255)                                          ttGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTGTATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTg                                                                      >  1:150477/1‑141 (MQ=255)                                          ttGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTg                                                                      >  1:165648/1‑141 (MQ=255)                                               tctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCTCATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                 <  1:120156/141‑1 (MQ=255)                                                 ttGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTtat                                                               <  1:108041/141‑1 (MQ=255)                                                     aTAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAtt                                                           <  1:112594/141‑1 (MQ=255)                                                                          gCAATAAAAGTACCACATCGCGTCAAAAAACCAGCATCTATATCCGTCATAATATGTCATAGTCCGGGCGTATATTTAACACCATTAATTGGATTATCACTTATCCTTGTATTAATAATCGAATTCATCTTATATATTaaa                                      >  2:34244/1‑141 (MQ=255)                                                                               aaaaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGTtcg                                 >  1:152640/1‑141 (MQ=255)                                                                                  aGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgtcg                              >  1:75189/1‑141 (MQ=255)                                                                                      acaaaacgcgTAAAAAAGCCAGCAACTAGATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGGCATTATTTGGATTATATCTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCt                          <  2:47947/135‑1 (MQ=255)                                                                                                 aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaatcata               >  2:38071/1‑140 (MQ=255)                                                                                                      aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTGTATTTTAAAGATCGTCGTGCTAAACAATAATGCACtt          <  1:122702/141‑1 (MQ=255)                                                                                                       aCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTa         <  2:164365/141‑1 (MQ=255)                                                                                                          aGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAg      >  1:5117/1‑141 (MQ=255)                                                                                                              tCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCTTACTAAACAATAATGCACTTAAATtttt  >  2:224883/1‑141 (MQ=255)                                                                                                                                     |                                                                                                                      ATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTT  >  USA300TCH1516_ALE/1513798‑1514047

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: ‑