# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Lepus_timidus/poplife/Ne/irl_Ne.txt /data/poplife/scratch/abernabe/Lepus_timidus/poplife/Ne/irl_19.vcf 26
# Running time:62.6646sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
26
# Genome size in Morgans:
26.00
# Total number of individuals in the input file:
20
# Effective Number of individuals included in the analysis (excluding missing genotypes):
17.60
# Number of SNPs in the input file:
360442
# Number of SNPs included in the analysis:
60982
# Number of SNP pairs included in the analysis:
1859371671
# Expected amount of raw data (= individuals x SNPs pairs):
37187433420
# Effective amount of raw data (may differ from the above one due to missing genotypes):
32719414102
# Proportion of missing data:
0.12014863
# 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):
0.51088141
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.13783758
# Observed d^2 of the sample (only between different cromosomes):
0.13776032
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.26178312
# Observed heterozygosity of individuals in the sample:
0.13387490
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 1859371671 pairs of SNPs.
# Ne point estimate:
105.28
# Lower bound of the 50% CI:
88.17
# Upper bound of the 50% CI:
125.72
# Lower bound of the 90% CI:
68.31
# Upper bound of the 90% CI:
162.28
# 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 1772514709 pairs of SNPs between chromosomes.
# Ne point estimate:
87.60
# Lower bound of the 50% CI:
71.03
# Upper bound of the 50% CI:
108.03
# Lower bound of the 90% CI:
52.54
# Upper bound of the 90% CI:
146.06
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
Not estimated because F value is too large
#