For instance, simultaneous analysis of thousands of SNPs have enabled genome-wide association studies for complex traits in chicken, pig cattle horse and sheep. In particular, SNPs are most suitable for whole genome association studies because linkage disequilibrium can be detected with high density SNP coverage of the genome when working with performance and production traits. Because of their potential for high genotyping efficiency, automation, data quality, genome-wide coverage and analytical simplicity, SNPs have rapidly become the marker of choice for many applications in genetics and genomics. Theoretically, SNPs can have four alleles in the population, but they most often exist as bi-allelic markers. They are among the most abundant type of genetic variations and widely distributed within genomes. Single nucleotide polymorphisms (SNPs) are alternative bases at any given position of DNA. Intra-specific SNPs in channel catfish = (1) + (3) + (5) Intra-specific SNPs in blue catfish = (2) + (3) + (6) Intra-specific SNPs shared by the two species = (3) Inter-specific SNPs between the two species = (4). (1) Intra-specific SNPs identified from positions where there were SNPs within channel catfish, but not within blue catfish (2) Intra-specific SNPs identified from positions where there were SNPs within blue catfish, but not within channel catfish (3) Intra-specific SNPs identified from positions where there were SNPs within both channel catfish and blue catfish (4) Inter-specific SNPs identified from positions where there were no SNPs in channel catfish or in blue catfish, but the sequence differed between the two species (5) Intra-specific SNPs identified from positions where there were SNPs within channel catfish and there were fewer than four blue catfish sequences (6) Intra-specific SNPs identified from positions where there were SNPs within blue catfish and there were fewer than four channel catfish sequences.
Additional file 2 Categorization of different types of SNPs identified from the all catfish assembly.
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