# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Apis_mellifera/poplife/Ne/Y_Ne.txt /data/poplife/scratch/abernabe/Apis_mellifera/poplife/Ne/Y_19.vcf 8
# Running time:42346.9sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
8
# Genome size in Morgans:
8.00
# Total number of individuals in the input file:
9
# Effective Number of individuals included in the analysis (excluding missing genotypes):
8.82
# Number of SNPs in the input file:
1900000
# Number of SNPs included in the analysis:
1231945
# Number of SNP pairs included in the analysis:
758843625540
# Expected amount of raw data (= individuals x SNPs pairs):
6829592629860
# Effective amount of raw data (may differ from the above one due to missing genotypes):
6694427676123
# Proportion of missing data:
0.01979107
# 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):
0.04519342
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.12937854
# Observed d^2 of the sample (only between different cromosomes):
0.12918566
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.28322919
# Observed heterozygosity of individuals in the sample:
0.28737128
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 758843625540 pairs of SNPs.
# Ne point estimate:
87.60
# Lower bound of the 50% CI:
73.13
# Upper bound of the 50% CI:
104.94
# Lower bound of the 90% CI:
56.39
# Upper bound of the 90% CI:
136.09
# 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 654842447570 pairs of SNPs between chromosomes.
# Ne point estimate:
55.32
# Lower bound of the 50% CI:
42.32
# Upper bound of the 50% CI:
72.32
# Lower bound of the 90% CI:
28.78
# Upper bound of the 90% CI:
106.34
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
0.00
#