# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Apis_mellifera/poplife/Ne/C_Ne.txt /data/poplife/scratch/abernabe/Apis_mellifera/poplife/Ne/C_19.vcf 14
# Running time:39592.8sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
14
# Genome size in Morgans:
14.00
# Total number of individuals in the input file:
9
# Effective Number of individuals included in the analysis (excluding missing genotypes):
8.00
# Number of SNPs in the input file:
1900000
# Number of SNPs included in the analysis:
1471408
# Number of SNP pairs included in the analysis:
1082520015528
# Expected amount of raw data (= individuals x SNPs pairs):
9742680139752
# Effective amount of raw data (may differ from the above one due to missing genotypes):
8655937652862
# Proportion of missing data:
0.11154451
# 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):
0.04176043
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.13794576
# Observed d^2 of the sample (only between different cromosomes):
0.13780571
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.22368024
# Observed heterozygosity of individuals in the sample:
0.20528416
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 1082520015528 pairs of SNPs.
# Ne point estimate:
158.24
# Lower bound of the 50% CI:
118.86
# Upper bound of the 50% CI:
210.68
# Lower bound of the 90% CI:
78.74
# Upper bound of the 90% CI:
318.02
# 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 993840477304 pairs of SNPs between chromosomes.
# Ne point estimate:
116.68
# Lower bound of the 50% CI:
79.60
# Upper bound of the 50% CI:
171.04
# Lower bound of the 90% CI:
45.91
# Upper bound of the 90% CI:
296.55
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
0.00
#