# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/eth_Ne.txt /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/eth_19.vcf 5
# Running time:4783.54sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
5
# Genome size in Morgans:
5.00
# 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:
1579431
# Number of SNP pairs included in the analysis:
1247300352165
# Expected amount of raw data (= individuals x SNPs pairs):
3741901056495
# Effective amount of raw data (may differ from the above one due to missing genotypes):
3741901056495
# 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):
-0.17911341
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.21578764
# Observed d^2 of the sample (only between different cromosomes):
0.21443731
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.38423774
# Observed heterozygosity of individuals in the sample:
0.52486961
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 1247300352165 pairs of SNPs.
# Ne point estimate:
2029.20
# Lower bound of the 50% CI:
674.18
# Upper bound of the 50% CI:
6107.66
# Lower bound of the 90% CI:
138.05
# Upper bound of the 90% CI:
29827.68
# 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 966236642543 pairs of SNPs between chromosomes.
# Ne point estimate:
100010000.00
# Lower bound of the 50% CI:
15152601.71
# Upper bound of the 50% CI:
660084670.25
# Lower bound of the 90% CI:
1002937.79
# Upper bound of the 90% CI:
9980049895.11
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
Not estimated because F value is too large
#
# Full sibling pairs (individuals are referenced by their ordinals in the ped file):
# Full-sibs not predicted because F value is too large.
#