BDOSE v1.0 file format

• Header

Bytes	Description
8	Magic number (bdose1.0)
4	Unsigned integer indicating the length LBGEN_filename in bytes of the BGEN filename used to generate the BDOSE file
LBGEN_filename	Name of the BGEN file
8	Unsigned integer indicating the size SBGEN_file of the BGEN file in bytes
Min(1000, SBGEN_file)	First bytes of the BGEN file
8	Unsigned integer indicating the size SBDOSE_file of the BDOSE file in bytes
4	Unsigned integer indicating the number of samples NSamples in the BDOSE file
4	Unsigned integer indicating the number of SNPs NSNPs in the BDOSE file

• SNP identifiers from Z file (sequence of N_SNPs blocks)

Bytes	Description
4	Unsigned integer indicating the length LBlock of the SNP identifier block in bytes
4	Unsigned integer indicating the line in which the SNP appears in the Z file
2	Unsigned integer indicating the length Lrsid of the entry in column rsid of the Z file in bytes
Lrsid	Entry in column rsid of the Z file
4	Unsigned integer indicating the entry in column position of the Z file
2	Unsigned integer indicating the length Lchromosome of the entry in column chromosome of the Z file in bytes
Lchromosome	Entry in column chromosome of the Z file
4	Unsigned integer indicating the length Lallele1 of the entry in column allele1 of the Z file in bytes
Lallele1	Entry in column allele1 of the Z file
4	Unsigned integer indicating the length Lallele2 of the entry in column allele2 of the Z file in bytes
Lallele2	Entry in column allele2 of the Z file
LBlock = 20 + Lrsid + Lchromosome + Lallele1 + Lallele2 number of bytes for the SNP identifier block

• Sample missingness

Bytes	Description
4 × NSNPs	Unsigned integers representing the missing data rate for each SNP

• Dosage data offsets

Bytes	Description
8 × NSNPs	Unsigned integers indicating the start position of dosages data for each SNP

• Dosage data

Bytes	Description
8 × NSamples	Floating-point numbers representing standardized dosages with respect to the allele in column allele2 of the Z file