# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Lepus_timidus/poplife/Ne/alp_Ne.txt /data/poplife/scratch/abernabe/Lepus_timidus/poplife/Ne/alp_19.vcf 26
# Running time:143.999sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
26
# Genome size in Morgans:
26.00
# Total number of individuals in the input file:
16
# Effective Number of individuals included in the analysis (excluding missing genotypes):
13.44
# Number of SNPs in the input file:
445493
# Number of SNPs included in the analysis:
104302
# Number of SNP pairs included in the analysis:
5439401451
# Expected amount of raw data (= individuals x SNPs pairs):
87030423216
# Effective amount of raw data (may differ from the above one due to missing genotypes):
73094176937
# Proportion of missing data:
0.16013074
# 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):
0.58397897
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.22147126
# Observed d^2 of the sample (only between different cromosomes):
0.22137951
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.23039552
# Observed heterozygosity of individuals in the sample:
0.10040278
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 5439401451 pairs of SNPs.
# Ne point estimate:
25.30
# Lower bound of the 50% CI:
22.33
# Upper bound of the 50% CI:
28.65
# Lower bound of the 90% CI:
18.66
# Upper bound of the 90% CI:
34.28
# 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 5183095968 pairs of SNPs between chromosomes.
# Ne point estimate:
22.22
# Lower bound of the 50% CI:
19.11
# Upper bound of the 50% CI:
25.83
# Lower bound of the 90% CI:
15.39
# Upper bound of the 90% CI:
32.09
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
Not estimated because F value is too large
#