# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Oryza_sativa/poplife/Ne/basmati_sadri_Ne.txt /data/poplife/scratch/abernabe/Oryza_sativa/poplife/Ne/basmati_sadri_19.vcf 12
# Running time:99.6704sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
12
# Genome size in Morgans:
12.00
# 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:
1690695
# Number of SNPs included in the analysis:
139662
# Number of SNP pairs included in the analysis:
9752667291
# Expected amount of raw data (= individuals x SNPs pairs):
48763336455
# Effective amount of raw data (may differ from the above one due to missing genotypes):
48763336455
# 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:
Not estimated because F value is too large
#
# OUTPUT PARAMETERS:
# Estimated F value of the population (deviation from H-W proportions):
0.84635100
# Observed d^2 of the sample (weighted correlation of loci pairs):
1.12264218
# Observed d^2 of the sample (only between different cromosomes):
1.08687198
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.35510805
# Observed heterozygosity of individuals in the sample:
0.06691727
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 9752667291 pairs of SNPs.
# Ne point estimate:
3.20
# Lower bound of the 50% CI:
5.01
# Upper bound of the 50% CI:
5.01
# Lower bound of the 90% CI:
5.01
# Upper bound of the 90% CI:
5.01
# 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 8882518332 pairs of SNPs between chromosomes.
# Ne point estimate:
3.20
# Lower bound of the 50% CI:
5.01
# Upper bound of the 50% CI:
5.01
# Lower bound of the 90% CI:
5.01
# Upper bound of the 90% CI:
5.01
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
Not estimated because F value is too large
#