# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Lepus_timidus/poplife/Ne/fsc_Ne.txt /data/poplife/scratch/abernabe/Lepus_timidus/poplife/Ne/fsc_19.vcf 26
# Running time:165.266sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
26
# Genome size in Morgans:
26.00
# Total number of individuals in the input file:
26
# Effective Number of individuals included in the analysis (excluding missing genotypes):
21.42
# Number of SNPs in the input file:
445397
# Number of SNPs included in the analysis:
82513
# Number of SNP pairs included in the analysis:
3404156328
# Expected amount of raw data (= individuals x SNPs pairs):
88508064528
# Effective amount of raw data (may differ from the above one due to missing genotypes):
72911378203
# Proportion of missing data:
0.17621769
# 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):
0.59370891
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.14245856
# Observed d^2 of the sample (only between different cromosomes):
0.14239530
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.16786807
# Observed heterozygosity of individuals in the sample:
0.06819391
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 3404156328 pairs of SNPs.
# Ne point estimate:
36.54
# Lower bound of the 50% CI:
33.15
# Upper bound of the 50% CI:
40.27
# Lower bound of the 90% CI:
28.82
# Upper bound of the 90% CI:
46.32
# 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 3244902361 pairs of SNPs between chromosomes.
# Ne point estimate:
33.94
# Lower bound of the 50% CI:
30.09
# Upper bound of the 50% CI:
38.27
# Lower bound of the 90% CI:
25.31
# Upper bound of the 90% CI:
45.51
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
Not estimated because F value is too large
#