STATISTICS ON SNPEFF ANNOTATION

Total number of probes:	485015
Number of probes annotated near/in genes	107746  (22.21%)

Distribitions of SNPeff annotations out of all probes:

frameshift_variant&stop_lost&splice_region_variant	4  (0.00%)	HIGH	HIGH
frameshift_variant&stop_gained	10  (0.00%)	HIGH	HIGH
disruptive_inframe_insertion	35  (0.01%)	MODERATE	
intergenic_region	376252  (77.58%)	MODIFIER	
splice_acceptor_variant&splice_region_variant&intron_variant	1  (0.00%)	HIGH	LOW
frameshift_variant&splice_region_variant	9  (0.00%)	HIGH	LOW
frameshift_variant&start_lost	2  (0.00%)	HIGH	HIGH
stop_lost&splice_region_variant	25  (0.01%)	HIGH	LOW
initiator_codon_variant	4  (0.00%)	LOW	
stop_gained	395  (0.08%)	HIGH	
splice_acceptor_variant&intron_variant	65  (0.01%)	HIGH	MODIFIER
splice_acceptor_variant&splice_region_variant&disruptive_inframe_deletion&intron_variant	1  (0.00%)	HIGH	LOW
stop_retained_variant	3  (0.00%)	LOW	
splice_donor_variant&intron_variant	67  (0.01%)	HIGH	MODIFIER
frameshift_variant&splice_acceptor_variant&splice_region_variant&intron_variant	1  (0.00%)	HIGH	HIGH
conservative_inframe_deletion	37  (0.01%)	MODERATE	
missense_variant	16677  (3.44%)	MODERATE	
missense_variant&splice_region_variant	219  (0.05%)	MODERATE	LOW
splice_region_variant&stop_retained_variant	13  (0.00%)	LOW	LOW
splice_region_variant&synonymous_variant	174  (0.04%)	LOW	LOW
splice_donor_variant&splice_region_variant&intron_variant	1  (0.00%)	HIGH	LOW
conservative_inframe_insertion	22  (0.00%)	MODERATE	
synonymous_variant	13521  (2.79%)	LOW	
splice_donor_variant&splice_region_variant&disruptive_inframe_deletion&intron_variant	2  (0.00%)	HIGH	LOW
splice_region_variant&intron_variant	997  (0.21%)	LOW	MODIFIER
stop_lost	11  (0.00%)	HIGH	
start_lost	20  (0.00%)	HIGH	
frameshift_variant&splice_donor_variant&splice_region_variant&intron_variant	1  (0.00%)	HIGH	HIGH
stop_gained&splice_region_variant	9  (0.00%)	HIGH	LOW
disruptive_inframe_deletion	74  (0.02%)	MODERATE	
downstream_gene_variant	17927  (3.70%)	MODIFIER	
upstream_gene_variant	16674  (3.44%)	MODIFIER	
frameshift_variant	399  (0.08%)	HIGH	
intron_variant	38598  (7.96%)	MODIFIER	
intragenic_variant	1748  (0.36%)	MODIFIER	

MODIFIER:	451199	93.04%
LOW:	13528	2.79%
MODERATE:	16845	3.48%
HIGH:	825	0.16%
ALT:	1601	0.33%


Distribitions of SNPeff annotations out of annotated probes:

frameshift_variant&stop_lost&splice_region_variant	4  (0.00%)	HIGH	HIGH
frameshift_variant&stop_gained	10  (0.01%)	HIGH	HIGH
disruptive_inframe_insertion	35  (0.03%)	MODERATE	
splice_acceptor_variant&splice_region_variant&intron_variant	1  (0.00%)	HIGH	LOW
frameshift_variant&splice_region_variant	9  (0.01%)	HIGH	LOW
frameshift_variant&start_lost	2  (0.00%)	HIGH	HIGH
stop_lost&splice_region_variant	25  (0.02%)	HIGH	LOW
initiator_codon_variant	4  (0.00%)	LOW	
stop_gained	395  (0.37%)	HIGH	
splice_acceptor_variant&intron_variant	65  (0.06%)	HIGH	MODIFIER
splice_acceptor_variant&splice_region_variant&disruptive_inframe_deletion&intron_variant	1  (0.00%)	HIGH	LOW
stop_retained_variant	3  (0.00%)	LOW	
splice_donor_variant&intron_variant	67  (0.06%)	HIGH	MODIFIER
frameshift_variant&splice_acceptor_variant&splice_region_variant&intron_variant	1  (0.00%)	HIGH	HIGH
conservative_inframe_deletion	37  (0.03%)	MODERATE	
missense_variant	16677  (15.48%)	MODERATE	
missense_variant&splice_region_variant	219  (0.20%)	MODERATE	LOW
splice_region_variant&stop_retained_variant	13  (0.01%)	LOW	LOW
splice_region_variant&synonymous_variant	174  (0.16%)	LOW	LOW
splice_donor_variant&splice_region_variant&intron_variant	1  (0.00%)	HIGH	LOW
conservative_inframe_insertion	22  (0.02%)	MODERATE	
synonymous_variant	13521  (12.55%)	LOW	
splice_donor_variant&splice_region_variant&disruptive_inframe_deletion&intron_variant	2  (0.00%)	HIGH	LOW
splice_region_variant&intron_variant	997  (0.93%)	LOW	MODIFIER
stop_lost	11  (0.01%)	HIGH	
start_lost	20  (0.02%)	HIGH	
frameshift_variant&splice_donor_variant&splice_region_variant&intron_variant	1  (0.00%)	HIGH	HIGH
stop_gained&splice_region_variant	9  (0.01%)	HIGH	LOW
disruptive_inframe_deletion	74  (0.07%)	MODERATE	
downstream_gene_variant	17927  (16.64%)	MODIFIER	
upstream_gene_variant	16674  (15.48%)	MODIFIER	
frameshift_variant	399  (0.37%)	HIGH	
intron_variant	38598  (35.82%)	MODIFIER	
intragenic_variant	1748  (1.62%)	MODIFIER	

MODIFIER:	74947	69.56%
LOW:	13528	12.55%
MODERATE:	16845	15.63%
HIGH:	825	0.77%
ALT:	1601	1.47%