# (currentNe v1.0)
# Command: /data/poplife/scratch/abernabe/currentNe/currentNe -t 8 -o /data/poplife/scratch/abernabe/Oryza_sativa/poplife/Ne/indica_Ne.txt /data/poplife/scratch/abernabe/Oryza_sativa/poplife/Ne/indica_19.vcf 4
# Running time:733.977sec
#
# INPUT PARAMETERS:
# Number of chromosomes in .map file:
4
# Genome size in Morgans:
4.00
# Total number of individuals in the input file:
85
# Effective Number of individuals included in the analysis (excluding missing genotypes):
62.45
# Number of SNPs in the input file:
1900000
# Number of SNPs included in the analysis:
85423
# Number of SNP pairs included in the analysis:
3648501753
# Expected amount of raw data (= individuals x SNPs pairs):
310122649005
# Effective amount of raw data (may differ from the above one due to missing genotypes):
227832158930
# Proportion of missing data:
0.26534821
# 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):
0.70063932
# Observed d^2 of the sample (weighted correlation of loci pairs):
0.07089215
# Observed d^2 of the sample (only between different cromosomes):
0.06624687
# Expected heterozygosity of individuals in the sample under H-W eq.:
0.08304060
# Observed heterozygosity of individuals in the sample:
0.02452449
#
# Ne estimation by integration over the whole genome (no genetic map available).
# Based on 3648501753 pairs of SNPs.
# Ne point estimate:
90.40
# Lower bound of the 50% CI:
87.68
# Upper bound of the 50% CI:
93.20
# Lower bound of the 90% CI:
83.91
# Upper bound of the 90% CI:
97.39
# 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 2471054539 pairs of SNPs between chromosomes.
# Ne point estimate:
47.84
# Lower bound of the 50% CI:
45.34
# Upper bound of the 50% CI:
50.48
# Lower bound of the 90% CI:
41.97
# Upper bound of the 90% CI:
54.53
# Estimated Number of full siblings that a random individuals has in the population (c=0.5):
Not estimated because F value is too large
#