# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/mon_Ne.txt /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/mon_19.vcf 7
# Running time:3570.54sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
7
# Genome size in Morgans:
7.00
# Total number of individuals in the input file:
2
# Effective Number of individuals included in the analysis (excluding missing genotypes):
2.00
# Number of SNPs in the input file:
1900000
# Number of SNPs included in the analysis:
1582349
# Number of SNP pairs included in the analysis:
1251913387726
# Expected amount of raw data (= individuals x SNPs pairs):
2503826775452
# Effective amount of raw data (may differ from the above one due to missing genotypes):
2503826775452
# 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):
-0.00560384
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.43783970
# Observed d^2 of the sample (only between different cromosomes):
0.43618963
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.41467069
# Observed heterozygosity of individuals in the sample:
0.55495595
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 1251913387726 pairs of SNPs.
# Ne point estimate:
100020000.00
# Lower bound of the 50% CI:
15155130.08
# Upper bound of the 50% CI:
660106534.49
# Lower bound of the 90% CI:
1002463.10
# Upper bound of the 90% CI:
9972073305.36
# 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 1061239661849 pairs of SNPs between chromosomes.
# Ne point estimate:
100010000.00
# Lower bound of the 50% CI:
15151874.88
# Upper bound of the 50% CI:
660116333.92
# Lower bound of the 90% CI:
1002820.47
# Upper bound of the 90% CI:
9981217679.80
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
0.00
#