# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Apis_mellifera/poplife/Ne/M_Ne.txt /data/poplife/scratch/abernabe/Apis_mellifera/poplife/Ne/M_19.vcf 10
# Running time:20753.9sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
10
# Genome size in Morgans:
10.00
# Total number of individuals in the input file:
9
# Effective Number of individuals included in the analysis (excluding missing genotypes):
8.80
# Number of SNPs in the input file:
1900000
# Number of SNPs included in the analysis:
1409152
# Number of SNP pairs included in the analysis:
992853974976
# Expected amount of raw data (= individuals x SNPs pairs):
8935685774784
# Effective amount of raw data (may differ from the above one due to missing genotypes):
8740602262199
# Proportion of missing data:
0.02183196
# 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:
0.22
#
# OUTPUT PARAMETERS:
# Estimated F value of the population (deviation from H-W proportions):
0.07207589
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.17486817
# Observed d^2 of the sample (only between different cromosomes):
0.17468281
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.26116038
# Observed heterozygosity of individuals in the sample:
0.25763521
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 992853974976 pairs of SNPs.
# Ne point estimate:
10.40
# Lower bound of the 50% CI:
9.57
# Upper bound of the 50% CI:
11.30
# Lower bound of the 90% CI:
8.49
# Upper bound of the 90% CI:
12.74
# Estimated Number of full siblings that a random individuals has in the population:
0.29
#
#
# Ne estimation based only on LD between chromosomes:
# Based on 882233210669 pairs of SNPs between chromosomes.
# Ne point estimate:
8.58
# Lower bound of the 50% CI:
7.54
# Upper bound of the 50% CI:
9.77
# Lower bound of the 90% CI:
6.26
# Upper bound of the 90% CI:
11.76
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
0.24
#
# Full sibling pairs (individuals are referenced by their ordinals in the ped file):
7, 8
#