Sequence coverage of PRNP in U.S. beef and dairy cattle. A. Physical map of PRNP that was sequenced in 192 beef and dairy cattle (25.2 kb) on 24 overlapping amplicons (blue bars). Orange and yellow color arrows represent untranslated and coding regions, respectively. B. Overall quality of PRNP sequence coverage. PRNP nucleotide sequence. with a phred score greater than 20 from at least two sequencing reads from the same animal was mapped to the corresponding nucleotide on a reference sequence [GenBank:AJ298878]. The blue line depicts the sequence quality of the 192 haploid cattle genomes comprising MBCDP2.1, the red line represents the 192 haploid cattle genomes comprising MDCP1.5, and the black line represents all 384 genomes combined. C. Close-up of PRNP sequence quality in an arbitrarily selected 2-kb window. Vertical arrows represent the location of polymorphisms (black for SNPs and white for indels). Polymorphisms with high minor allele frequencies are reflected by dips in sequence quality that correspond with heterozygous animals. The low phred score locus approximately at 48.5 kb is the result of animals heterozygous for two indels.
Clawson et al. BMC Genetics 2006 7:51 doi:10.1186/1471-2156-7-51