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Table 1 List of filtering rules used for identification of sex-linked contigs; filtering rules for identification of X-linked genes following segregation pattern A

From: Fully automated pipeline for detection of sex linked genes using RNA-Seq data

Mother must be homozygous (X 1 X 1 ). Especially is checked whether mother contains any father variants (X2). Limited tolerance of these variants is described in Table 3.
Sons must be same as mother (X 1 ). First, we have to exclude male variants (variants shared between father and son but absent in daughter). Then, sons must contain only X1 variants of mother.
Father must differ from mother. Father must have at least one SNP (X2) in which it differs from mother.
Daughters must have mother and father alleles (X 1 X 2 ). Only heterozygous daughter contigs are taken into account. These daughter variants must be subset of father variants.
Daughters and sons cannot have any intersection. Sons are tested if they contain daughter variants with tolerance described in Table 3. Similarly, daughters are tested for presence of son variants.
Sufficient coverage. Average depth per nucleotide must be at least 0.75 (=in contig of length 100, there must be at least 75 nucleotides present/mapped).