STATISTICS ON SNPEFF ANNOTATION

Total number of probes:	200000
Number of probes annotated near/in genes	48054  (24.03%)

Distribitions of SNPeff annotations out of all probes:

splice_region_variant&synonymous_variant	60  (0.03%)	LOW	LOW
frameshift_variant&stop_lost&splice_region_variant	1  (0.00%)	HIGH	HIGH
frameshift_variant&stop_gained	3  (0.00%)	HIGH	HIGH
disruptive_inframe_insertion	15  (0.01%)	MODERATE	
intergenic_region	151946  (75.97%)	MODIFIER	
splice_donor_variant&splice_region_variant&intron_variant	1  (0.00%)	HIGH	LOW
frameshift_variant&splice_region_variant	2  (0.00%)	HIGH	LOW
frameshift_variant&start_lost	1  (0.00%)	HIGH	HIGH
conservative_inframe_insertion	12  (0.01%)	MODERATE	
synonymous_variant	5873  (2.94%)	LOW	
stop_lost&splice_region_variant	8  (0.00%)	HIGH	LOW
splice_donor_variant&splice_region_variant&disruptive_inframe_deletion&intron_variant	1  (0.00%)	HIGH	LOW
stop_gained	149  (0.07%)	HIGH	
splice_acceptor_variant&intron_variant	25  (0.01%)	HIGH	MODIFIER
splice_region_variant&intron_variant	303  (0.15%)	LOW	MODIFIER
stop_retained_variant	1  (0.00%)	LOW	
stop_lost	3  (0.00%)	HIGH	
start_lost	9  (0.00%)	HIGH	
splice_donor_variant&intron_variant	21  (0.01%)	HIGH	MODIFIER
stop_gained&splice_region_variant	3  (0.00%)	HIGH	LOW
conservative_inframe_deletion	14  (0.01%)	MODERATE	
disruptive_inframe_deletion	22  (0.01%)	MODERATE	
downstream_gene_variant	8087  (4.04%)	MODIFIER	
missense_variant	6433  (3.22%)	MODERATE	
upstream_gene_variant	7251  (3.63%)	MODIFIER	
frameshift_variant	133  (0.07%)	HIGH	
intron_variant	18574  (9.29%)	MODIFIER	
missense_variant&splice_region_variant	73  (0.04%)	MODERATE	LOW
intragenic_variant	966  (0.48%)	MODIFIER	
splice_region_variant&stop_retained_variant	10  (0.01%)	LOW	LOW

MODIFIER:	186824	93.41%
LOW:	5874	2.94%
MODERATE:	6496	3.26%
HIGH:	294	0.14%
ALT:	512	0.25%


Distribitions of SNPeff annotations out of annotated probes:

splice_region_variant&synonymous_variant	60  (0.12%)	LOW	LOW
frameshift_variant&stop_lost&splice_region_variant	1  (0.00%)	HIGH	HIGH
frameshift_variant&stop_gained	3  (0.01%)	HIGH	HIGH
disruptive_inframe_insertion	15  (0.03%)	MODERATE	
splice_donor_variant&splice_region_variant&intron_variant	1  (0.00%)	HIGH	LOW
frameshift_variant&splice_region_variant	2  (0.00%)	HIGH	LOW
frameshift_variant&start_lost	1  (0.00%)	HIGH	HIGH
conservative_inframe_insertion	12  (0.02%)	MODERATE	
synonymous_variant	5873  (12.22%)	LOW	
stop_lost&splice_region_variant	8  (0.02%)	HIGH	LOW
splice_donor_variant&splice_region_variant&disruptive_inframe_deletion&intron_variant	1  (0.00%)	HIGH	LOW
stop_gained	149  (0.31%)	HIGH	
splice_acceptor_variant&intron_variant	25  (0.05%)	HIGH	MODIFIER
splice_region_variant&intron_variant	303  (0.63%)	LOW	MODIFIER
stop_retained_variant	1  (0.00%)	LOW	
stop_lost	3  (0.01%)	HIGH	
start_lost	9  (0.02%)	HIGH	
splice_donor_variant&intron_variant	21  (0.04%)	HIGH	MODIFIER
stop_gained&splice_region_variant	3  (0.01%)	HIGH	LOW
conservative_inframe_deletion	14  (0.03%)	MODERATE	
disruptive_inframe_deletion	22  (0.05%)	MODERATE	
downstream_gene_variant	8087  (16.83%)	MODIFIER	
missense_variant	6433  (13.39%)	MODERATE	
upstream_gene_variant	7251  (15.09%)	MODIFIER	
frameshift_variant	133  (0.28%)	HIGH	
intron_variant	18574  (38.65%)	MODIFIER	
missense_variant&splice_region_variant	73  (0.15%)	MODERATE	LOW
intragenic_variant	966  (2.01%)	MODIFIER	
splice_region_variant&stop_retained_variant	10  (0.02%)	LOW	LOW

MODIFIER:	34878	72.58%
LOW:	5874	12.22%
MODERATE:	6496	13.52%
HIGH:	294	0.62%
ALT:	512	1.05%