Two Japanese reference genomes (JRG v1 and decoyJRGv1) are available.
Please select suitable reference genome with your analysis.
(“*” is version number.)

JRG v*: if you need to keep GRCh38 coordinate in your analysis

Please download GRCh38decoyJRGv*.fasta
The fasta file contains chr1-22, chrX, chrY, chrM and decoyJRGv*.
Chromosomes chr1-22, chrX, chrY and chrM except for decoyJRGv* are the same to GRCh38 reference.
If you use this assembly instead of GRCh38, you can avoid the misalignment to chromosomes in GRCh38.
Hence, the user can use many annotation database of GRCh38.
If you just have interest for the decoy sequence, please download decoyJRGv*.fasta.

decoyJRG v*: If you use the best Japanese reference coordinate in your analysis

Please download JRGv*.fasta
If you use the assembly instead of GRCh38, you can find new SNVs and insertions in the newly integrated insertions.
The fasta file contains chr1-22, chrX, chrY and chrM. Each chromosome except for chrM has novel insertions integrated to GRCh38.
The extended length for each chromosome in JRGv1 to GRCh38 chromosome is summarized in statistics.
The absolute coordinates between GRCh38 and JRGv* are different and since reannotation to the JRGv* coordinate is required, e.g. using a tool lifetover.