# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/som_Ne.txt /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/som_19.vcf 4
# Running time:10684.2sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
4
# Genome size in Morgans:
4.00
# Total number of individuals in the input file:
5
# Effective Number of individuals included in the analysis (excluding missing genotypes):
5.00
# Number of SNPs in the input file:
1900000
# Number of SNPs included in the analysis:
1655645
# Number of SNP pairs included in the analysis:
1370579355190
# Expected amount of raw data (= individuals x SNPs pairs):
6852896775950
# Effective amount of raw data (may differ from the above one due to missing genotypes):
6852896775950
# 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:
0.40
#
# OUTPUT PARAMETERS:
# Estimated F value of the population (deviation from H-W proportions):
-0.05902496
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.18389096
# Observed d^2 of the sample (only between different cromosomes):
0.18399367
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.32682592
# Observed heterozygosity of individuals in the sample:
0.38206850
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 1370579355190 pairs of SNPs.
# Ne point estimate:
283079.95
# Lower bound of the 50% CI:
47329.84
# Upper bound of the 50% CI:
1693102.28
# Lower bound of the 90% CI:
3607.24
# Upper bound of the 90% CI:
22199317.01
# Estimated Number of full siblings that a random individuals has in the population:
28307.99
#
#
# Ne estimation based only on LD between chromosomes:
# Based on 1022756227869 pairs of SNPs between chromosomes.
# Ne point estimate:
205892.87
# Lower bound of the 50% CI:
32087.11
# Upper bound of the 50% CI:
1321149.68
# Lower bound of the 90% CI:
2211.75
# Upper bound of the 90% CI:
19166634.72
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
20589.29
#
# Full sibling pairs (individuals are referenced by their ordinals in the ped file):
1, 2
#