3.1 Input formats

3.1.1 Genotype

Hapmap

TABLE 3.1: Hapmap format

rs	alleles	chrom	pos	strand	assembly	center	protLSID	assayLSID
SNP_1	A/C	1	1000		AGPv1	Panzea	NA	NA
SNP_2	C/G	1	1010		AGPv1	Panzea	NA	NA
SNP_3	G/T	1	1020		AGPv1	Panzea	NA	NA

TABLE 3.1: Hapmap format (Continued)

panel	QCcode	ID_1	ID_2	ID_3
nam	NA	CC	NA	AC
nam	NA	CC	GG	CC
nam	NA	GG	GG	TT

VCF

Reference

TABLE 3.2: VCF format

CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	1000	SNP_1	A	C	29	PASS	NS=3;DP=14;AF=0.5;DB;H2
1	1010	SNP_2	C	G	3	q10	NS=3;DP=11;AF=0.017
1	1020	SNP_3	G	T	67	PASS	NS=2;DP=10;AF=0.333,0.667

TABLE 3.2: VCF format (Continued)

FORMAT	ID_1	ID_2	ID_3
GT:GQ:DP:HQ	1|1:48:1:51,51	.|.:8:8:51,51	0/1:43:5:.,.
GT:GQ:DP:HQ	0|0:49:3:58,50	1|1:3:5:65,3	0/0:41:3
GT:GQ:DP:HQ	0|0:21:6:23,27	0|0:2:0:18,2	1/1:35:4

Numerical Data

TABLE 3.3: Numerical format

taxa	SNP_1	SNP_2	SNP_3
ID_1	2	0	0
ID_2	NA	2	0
ID_3	2	0	0

PLINK

Reference

Missing values must be assigned as 0

TABLE 3.4: PLINK format

ID_1	ID_1	0	0	0	0	C C	C C	G G
ID_2	ID_2	0	0	0	0	0 0	G G	G G
ID_3	ID_3	0	0	0	0	A C	C C	T T

3.1.2 Phenotype

TABLE 3.5: Phenotype format

taxa	y75	y50	y25
ID_1	-1.261850849964	-9.91585546798912	-6.36283902912281
ID_2	2.59372569418469	-6.51298727967311	2.29326112214355
ID_3	2.91265183779147	-22.1380297243291	19.6659577252647
…	…	…	…

3.1.3 Map

TABLE 3.6: SNPs Map for numerical formats

SNP	Chromosome	Position
SNP_1	1	1000
SNP_2	1	1010
SNP_3	1	1020
…	…	…

TABLE 3.7: SNPs Map for PLINK formats

1	SNP_1	0	1000
1	SNP_2	0	1010
1	SNP_3	0	1020
…	…	…	…

3.1.4 Covariates

TABLE 3.8: Covariates format

Taxa	Cov1	Cov2
ID_1	3.617538	-0.9368706
ID_2	0.888413	-0.0546190
ID_3	-1.276830	0.2140963

3.1.5 Kinship

TABLE 3.9: Kinship format

1.7675808170611	0.0312931060706081	0.0584911825909184	…
0.0312931060706081	1.85921066074289	0.0206883855892893	…
0.0584911825909184	0.0206883855892893	1.88643105515969	…
…	…	…	…