A simple procedure for directly obtaining haplotype sequences of diploid genomes

BMC Genomics

Table 5 Descriptive statistics for SNP containing haploid sequences constructed by SIH averaged over all autosomes

Sample Set¹	Mean haplotype length (kbp)	N50 haplotype length (kbp)	Max haplotype length (kbp)	% SNP phased	% Genes Within haplotypes	% Genome in haplotype blocks
Angus Steer CM	43	97	738	88	38	64
Angus Steer TC	82	190	946	87	46	68
EAZ Cells CM	39	105	921	34	19	27
EAZ Cells TC	84	201	1653	30	42	32
EAZ Fosmids CM	65	134	1194	82	23	57
EAZ Fosmids TC	127	257	2457	80	48	66
Angus Bull CM	72	155	1243	31	12	22
Angus Bull TC	229	1142	7.878	53	14	38

¹The low proportion of genome covered by the Angus Bull SNP haplotypes compared to the high genome coverage of scaffolds was partly due to a large proportion of scaffolds containing heterozygotes that were filtered prior to haplotype construction. For the Angus bull no scaffolds were used that contained heterozygotes, for the other sample sets scaffolds with a maximum of 3 heterozygotes or a maximum of 20 % heterozygotes were accepted and the heterozygous positions deleted

ISSN: 1471-2164