Index of /pub/For_Seq_Analysis

	Name	Last modified	Size	Description
	Parent Directory		-
	README.txt	2020-03-16 17:02	1.5K
	fasta_files/	2020-03-16 17:02	-
	list_of_variations/	2020-03-16 17:02	-

[fasta_files]
Fasta files of MSMv3 and JF1v2 were generated by Samtools (ver 0.1.16) pileup function (ignore BAQ（-B）option). Detection of SNPs and indels between MSM/JF1 and B6 was described in Takada et al. GENOME RESEARCH (2013).
    In the fasta files, "N or n" stands for nucleotides unmapped onto the reference B6 and ambiguous call of genotypes. Small letter stands for SNPs called as low confidential sequences (less than 3 and more than 30 reads in MSM, and less than 15 and more than 59 reads in JF1). These SNPs were ignored for counting of variations in the analysis. When two or more genotypes were observed at the same location, the nucleotide location was designated as IUB code. Capital letter of IUB code indicates that the read number of the 2nd major genotype exceeded 30% of the total covered reads, and small letter indicates that the read number of the 2nd major genotype was less than 30% of the total covered reads. For variation of insertions and deletions, capital letter indicates that the read number of the major genotype exceeded 30% of the total covered reads, and small letter indicates that the read number of the major genotype was less than 30% of the total covered reads. 

[list_of_variations]
msmv3_Snp.tsv; list of B6 - MSM SNPs
msmv3_Snp_indel.tsv; list of B6 - MSM SNPs and indels
msmv3_indel.tsv; list of B6 - MSM indels
jf1v2_Snp.tsv; list of B6 - JF1 SNPs
jf1v2_Snp_indel.tsv; list of B6 - JF1 SNPs and indels
jf1v2_indel.tsv; list of B6 - JF1 indels

row
1. chromosome
2. start_position
3. end_ position
4. mm9
5. target