# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Apis_mellifera/poplife/Ne/A_Ne.txt /data/poplife/scratch/abernabe/Apis_mellifera/poplife/Ne/A_19.vcf 3
# Running time:93760.5sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
3
# Genome size in Morgans:
3.00
# Total number of individuals in the input file:
11
# Effective Number of individuals included in the analysis (excluding missing genotypes):
10.68
# Number of SNPs in the input file:
1900000
# Number of SNPs included in the analysis:
1719386
# Number of SNP pairs included in the analysis:
1478143248805
# Expected amount of raw data (= individuals x SNPs pairs):
16259575736855
# Effective amount of raw data (may differ from the above one due to missing genotypes):
15787843490435
# Proportion of missing data:
0.02901258
# 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):
0.07462557
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.11127349
# Observed d^2 of the sample (only between different cromosomes):
0.11110301
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.18333512
# Observed heterozygosity of individuals in the sample:
0.17824554
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 1478143248805 pairs of SNPs.
# Ne point estimate:
320.48
# Lower bound of the 50% CI:
265.56
# Upper bound of the 50% CI:
386.75
# Lower bound of the 90% CI:
202.63
# Upper bound of the 90% CI:
506.87
# 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 882785525863 pairs of SNPs between chromosomes.
# Ne point estimate:
106.59
# Lower bound of the 50% CI:
79.96
# Upper bound of the 50% CI:
142.08
# Lower bound of the 90% CI:
52.87
# Upper bound of the 90% CI:
214.85
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
0.00
#