Alternate-locus aware variant calling in whole genome sequencing

Table 2 Population-specific alternate loci

Alternate locus	FIN	LWK	CHB	PEL
chr4_KI270787v1_alt			\(\checkmark \)	\(\checkmark \)
chr5_GL383531v1_alt	\(\checkmark \)
chr5_GL949742v1_alt			\(\checkmark \)
chr6_GL383533v1_alt				\(\checkmark \)*
chr6_KI270801v1_alt		\(\checkmark \)	\(\checkmark \)	\(\checkmark \)*
chr9_GL383542v1_alt		\(\checkmark \)
chr11_JH159136v1_alt		\(\checkmark \)		\(\checkmark \)*
chr13_KI270839v1_alt	\(\checkmark \)		\(\checkmark \)	\(\checkmark \)*
chr14_KI270844v1_alt			\(\checkmark \)	\(\checkmark \)
chr15_GL383555v2_alt	\(\checkmark \)*		\(\checkmark \)	\(\checkmark \)*
chr18_GL383570v1_alt			\(\checkmark \)

Shown are all the alternate loci that were inferred to be present in at least 90% of the individuals of a population. Alternate loci present in all investigated individuals of the population are marked with an asterisk (*)
CHB Asian, Han Chinese in Beijing, China, FIN European, Finnish in Finland, LWK African, Luhya in Webuye, Kenya, PEL South Americans, Peruvians from Lima, Peru

ISSN: 1756-994X