Genome-wide homozygosity in Canine_hom_map_27_3_12 - Canine_hom_map_27_3_12_100-2_ped_copy

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score	chr	from (bp)	to (bp)	from SNP	to SNP	build 37
broad - use this when you expect some genetic heterogeneity
91	31	3470611	4086164	#121273	#22761	region	genotypes
82	30	3480121	3730100	#22278	#228805	region	genotypes
80	30	3870300	3930618	#22283	#228817	region	genotypes
79	30	3039134	3079262	#22271	#22272	region	genotypes
79	30	3111771	3128902	#228784	#22273	region	genotypes
79	30	3302865	3355581	#228790	#228793	region	genotypes
79	30	3373938	3457004	#228795	#228799	region	genotypes
narrow - use this when all patients are in the same family
91	31	3470611	4086164	#121273	#22761	region	genotypes
82	30	3480121	3730100	#22278	#228805	region	genotypes
80	30	3870300	3930618	#22283	#228817	region	genotypes
79	30	3039134	3079262	#22271	#22272	region	genotypes
79	30	3111771	3128902	#228784	#22273	region	genotypes
79	30	3302865	3355581	#228790	#228793	region	genotypes
79	30	3373938	3457004	#228795	#228799	region	genotypes

change threshold

0.99 x max 0.9 x max 0.8 x max 0.7 x max 0.6 x max 0.5 x max

create files for Alohomora
flanking region [bp] allele frequencies from all samples allele frequencies from controls allele frequencies equally distributed narrow regions broad regions

create a BED file build 37
complete homozygous regions shown here		narrow regions broad regions
complete genes within these only exons	flanked by bases on each side.

analysis settings
project_name	Canine_hom_map_27_3_12	change name
analysis_name	Canine_hom_map_27_3_12_100-2_ped_copy	change name
analysis_description	100-2 pedigree homozygosity mapping
max_block_length	80
max_score	91
user_login	ahramd
homogeneity_required	homogeneity required
lower_limit	0
date	2012-03-30 00:00:00
exclusion_length	250
cases	100-002,100-017,100-072
controls	100-001,100-013

retrieve homozyosity scores