# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/sud_Ne.txt /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/sud_19.vcf 5
# Running time:7474.93sec
#
# 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:
1708429
# Number of SNP pairs included in the analysis:
1459363969806
# Expected amount of raw data (= individuals x SNPs pairs):
4378091909418
# Effective amount of raw data (may differ from the above one due to missing genotypes):
4378091909418
# 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:
0.00
#
# OUTPUT PARAMETERS:
# Estimated F value of the population (deviation from H-W proportions):
0.01010336
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.32835693
# Observed d^2 of the sample (only between different cromosomes):
0.32803753
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.37407866
# Observed heterozygosity of individuals in the sample:
0.44525877
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 1459363969806 pairs of SNPs.
# Ne point estimate:
304.50
# Lower bound of the 50% CI:
165.46
# Upper bound of the 50% CI:
560.36
# Lower bound of the 90% CI:
68.80
# Upper bound of the 90% CI:
1347.71
# Estimated Number of full siblings that a random individuals has in the population:
0.00
#
#
# Ne estimation based only on LD between chromosomes:
# Based on 1161649708324 pairs of SNPs between chromosomes.
# Ne point estimate:
155.84
# Lower bound of the 50% CI:
63.83
# Upper bound of the 50% CI:
380.48
# Lower bound of the 90% CI:
17.67
# Upper bound of the 90% CI:
1374.76
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
0.00
#