# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/kaz_Ne.txt /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/kaz_19.vcf 7
# Running time:5754.84sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
7
# Genome size in Morgans:
7.00
# Total number of individuals in the input file:
2
# Effective Number of individuals included in the analysis (excluding missing genotypes):
2.00
# Number of SNPs in the input file:
1900000
# Number of SNPs included in the analysis:
1639332
# Number of SNP pairs included in the analysis:
1343703883446
# Expected amount of raw data (= individuals x SNPs pairs):
2687407766892
# Effective amount of raw data (may differ from the above one due to missing genotypes):
2687407766892
# Proportion of missing data:
0.00000000
# Number of full siblings that a random individuals has in the population:
Not given
## Number of full siblings that a random individuals has in the sample:
Not estimated because F value is too large
#
# OUTPUT PARAMETERS:
# Estimated F value of the population (deviation from H-W proportions):
0.08465039
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.55367897
# Observed d^2 of the sample (only between different cromosomes):
0.55382790
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.41214188
# Observed heterozygosity of individuals in the sample:
0.51761053
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 1343703883446 pairs of SNPs.
# Ne point estimate:
9.36
# Lower bound of the 50% CI:
7.24
# Upper bound of the 50% CI:
12.10
# Lower bound of the 90% CI:
5.01
# Upper bound of the 90% CI:
17.52
# Estimated Number of full siblings that a random individuals has in the population:
Not estimated because F value is too large
#
#
# Ne estimation based only on LD between chromosomes:
# Based on 1128644092084 pairs of SNPs between chromosomes.
# Ne point estimate:
7.98
# Lower bound of the 50% CI:
5.14
# Upper bound of the 50% CI:
12.39
# Lower bound of the 90% CI:
5.01
# Upper bound of the 90% CI:
23.32
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
Not estimated because F value is too large
#