Post by djoser-xyyman on Jul 6, 2019 16:07:10 GMT -5
Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing -
Masao Nagasaki
www.nature.com/articles/s41439-019-0057-7
quote:
Thus, the sequences discovered in this study represent the ancestral state, and insertions absent from the current reference genome assembly were derived from deletion events that occurred in the ancestral human population. The abundance of polymorphic novel insertions implies that there are a substantial number of undiscovered sequences, which are missing from not only the reference assembly (GRCh38) genome but also from JRGv0. The whole-genome sequence of GRCh38 was assembled by contigs from a relatively large number of individuals. If these individuals had a homozygous deletion at a locus, the sequence at that locus was missing from the reference genome assembly. This situation was more likely if the number of individuals contributing to the reference sequence (nref) was smaller and/or if the MAF of the inserted sequence (MAFins) was lower. To address this possibility, the discovery rates of novel insertions were estimated using the demographic model of the 1KJPN population12.
Masao Nagasaki
www.nature.com/articles/s41439-019-0057-7
quote:
Thus, the sequences discovered in this study represent the ancestral state, and insertions absent from the current reference genome assembly were derived from deletion events that occurred in the ancestral human population. The abundance of polymorphic novel insertions implies that there are a substantial number of undiscovered sequences, which are missing from not only the reference assembly (GRCh38) genome but also from JRGv0. The whole-genome sequence of GRCh38 was assembled by contigs from a relatively large number of individuals. If these individuals had a homozygous deletion at a locus, the sequence at that locus was missing from the reference genome assembly. This situation was more likely if the number of individuals contributing to the reference sequence (nref) was smaller and/or if the MAF of the inserted sequence (MAFins) was lower. To address this possibility, the discovery rates of novel insertions were estimated using the demographic model of the 1KJPN population12.