# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/egy_Ne.txt /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/egy_19.vcf 6
# Running time:6261.57sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
6
# Genome size in Morgans:
6.00
# Total number of individuals in the input file:
3
# Effective Number of individuals included in the analysis (excluding missing genotypes):
3.00
# Number of SNPs in the input file:
1900000
# Number of SNPs included in the analysis:
1667256
# Number of SNP pairs included in the analysis:
1389870451140
# Expected amount of raw data (= individuals x SNPs pairs):
4169611353420
# Effective amount of raw data (may differ from the above one due to missing genotypes):
4169611353420
# 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:
0.00
#
# OUTPUT PARAMETERS:
# Estimated F value of the population (deviation from H-W proportions):
-0.07216942
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.30173195
# Observed d^2 of the sample (only between different cromosomes):
0.30129522
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.38092767
# Observed heterozygosity of individuals in the sample:
0.48312937
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 1389870451140 pairs of SNPs.
# Ne point estimate:
9.36
# Lower bound of the 50% CI:
7.87
# Upper bound of the 50% CI:
11.14
# Lower bound of the 90% CI:
6.13
# Upper bound of the 90% CI:
14.30
# Estimated Number of full siblings that a random individuals has in the population:
0.00
#
#
# Ne estimation based only on LD between chromosomes:
# Based on 1133736013020 pairs of SNPs between chromosomes.
# Ne point estimate:
7.98
# Lower bound of the 50% CI:
5.83
# Upper bound of the 50% CI:
10.92
# Lower bound of the 90% CI:
5.01
# Upper bound of the 90% CI:
17.14
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
0.00
#