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%	69.2 / NA	21	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (6/15);  total (6/15)

TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAA  >  USA300TCH1516_ALE/1513796‑1514041                                                                                                                                        |                                                                                                                ttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGat                                                                                                    <  4:408426/148‑1 (MQ=255)   ttttGTATGTATCGCTTTATGAGTAGCCATTGGCAGGGGGTTTGTCTCTTAGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatta                                                                                                  <  4:368255/147‑1 (MQ=255)          tgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGc                                                                                           >  3:364720/1‑148 (MQ=255)            tatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                         <  3:218558/148‑1 (MQ=255)            tatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                         <  3:310206/148‑1 (MQ=255)                  tttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGAATACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTAttt                                                                                   <  4:388337/148‑1 (MQ=255)                           agCCCTTAGGATGGGGTTTGGCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                 <  2:11196/141‑1 (MQ=255)                           agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                          <  3:25385/148‑1 (MQ=255)                           agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                          <  3:25386/148‑1 (MQ=255)                           agCCATTGGCATGGGATTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                          <  3:344846/148‑1 (MQ=255)                            gCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                          >  3:174672/1‑148 (MQ=255)                               aTTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                      <  4:147448/148‑1 (MQ=255)                                                     ggATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTGTCCTTGTATTTATAATTGAAtt                                                <  4:67127/148‑1 (MQ=255)                                                     ggATAAAGCGTACAAAAAATACTGCAATAAAAGTACAACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                <  4:103705/148‑1 (MQ=255)                                                     ggATAAAAAATACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                <  4:353049/148‑1 (MQ=255)                                                              gTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtata                                       >  4:155656/1‑148 (MQ=255)                                                              gTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtata                                       >  3:131372/1‑148 (MQ=255)                                                                                tAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                     <  4:283910/148‑1 (MQ=255)                                                                                     gTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAAc                <  3:385685/148‑1 (MQ=255)                                                                                                  t‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTa   >  3:73342/1‑148 (MQ=255)                                                                                                    aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa  >  4:75787/1‑148 (MQ=255)                                                                                                                                        |                                                                                                                TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAA  >  USA300TCH1516_ALE/1513796‑1514041

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑