# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/mau_Ne.txt /data/poplife/scratch/abernabe/Equus_asinus/poplife/Ne/mau_19.vcf 6
# Running time:6815.83sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
6
# Genome size in Morgans:
6.00
# 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:
1675812
# Number of SNP pairs included in the analysis:
1404172091766
# Expected amount of raw data (= individuals x SNPs pairs):
4212516275298
# Effective amount of raw data (may differ from the above one due to missing genotypes):
4212516275298
# 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):
0.00218460
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.32168153
# Observed d^2 of the sample (only between different cromosomes):
0.32175822
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.37257511
# Observed heterozygosity of individuals in the sample:
0.44630842
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 1404172091766 pairs of SNPs.
# Ne point estimate:
1496.40
# Lower bound of the 50% CI:
522.94
# Upper bound of the 50% CI:
4281.98
# Lower bound of the 90% CI:
115.25
# Upper bound of the 90% CI:
19436.46
# 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 1152738679156 pairs of SNPs between chromosomes.
# Ne point estimate:
657.74
# Lower bound of the 50% CI:
180.21
# Upper bound of the 50% CI:
2400.67
# Lower bound of the 90% CI:
27.99
# Upper bound of the 90% CI:
15457.77
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
0.00
#