# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Oryza_sativa/poplife/Ne/temperate_japonica_Ne.txt /data/poplife/scratch/abernabe/Oryza_sativa/poplife/Ne/temperate_japonica_19.vcf 6
# Running time:7919.28sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
6
# Genome size in Morgans:
6.00
# Total number of individuals in the input file:
54
# Effective Number of individuals included in the analysis (excluding missing genotypes):
40.18
# Number of SNPs in the input file:
1900000
# Number of SNPs included in the analysis:
370985
# Number of SNP pairs included in the analysis:
68814749620
# Expected amount of raw data (= individuals x SNPs pairs):
3715996479480
# Effective amount of raw data (may differ from the above one due to missing genotypes):
2764955561352
# Proportion of missing data:
0.25593160
# 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):
0.88672567
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.45139307
# Observed d^2 of the sample (only between different cromosomes):
0.42677222
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.10433965
# Observed heterozygosity of individuals in the sample:
0.01238794
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 68814749620 pairs of SNPs.
# Ne point estimate:
4.05
# 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 56757694042 pairs of SNPs between chromosomes.
# Ne point estimate:
4.05
# 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
#