view test-data/snpeff_stats.tabular @ 12:1c2db0054039 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984

Sample	MODERATE	splice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant_percent	splice_region_variant+non_coding_exon_variant	frameshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant_percent	frameshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant	splice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant	frameshift_variant+start_lost+splice_region_variant_percent	NONE	intragenic_variant_percent	splice_region_variant+non_coding_exon_variant_percent	UTR_3_PRIME	splice_donor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent	splice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant	Ts_Tv_ratio	splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent	inframe_insertion+splice_region_variant_percent	UTR_3_PRIME_percent	inframe_deletion+splice_region_variant	5_prime_UTR_truncation+exon_loss_variant	disruptive_inframe_deletion_percent	INTRON	LOW	Het	start_lost+disruptive_inframe_insertion	frameshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant_percent	inframe_deletion	splice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent	non_coding_exon_variant	frameshift_variant+stop_gained	splice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent	DOWNSTREAM_percent	disruptive_inframe_deletion+splice_region_variant	MOTIF	frameshift_variant+start_lost+splice_region_variant	splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant	frameshift_variant+stop_gained_percent	EXON	splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant	upstream_gene_variant	intron_variant_percent	splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent	inframe_deletion_percent	HIGH_percent	3_prime_UTR_variant	splice_donor_variant+intron_variant	frameshift_variant+start_lost_percent	disruptive_inframe_insertion	non_coding_exon_variant_percent	Change_rate	5_prime_UTR_truncation+exon_loss_variant_percent	MODERATE_percent	splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent	UTR_5_PRIME	TRANSCRIPT	frameshift_variant	downstream_gene_variant	MODIFIER_percent	splice_acceptor_variant+inframe_deletion+splice_region_variant+splice_region_variant+intron_variant_percent	LOW_percent	frameshift_variant+splice_region_variant	Missense_Silent_ratio	Missing	disruptive_inframe_deletion+splice_region_variant_percent	splice_acceptor_variant+disruptive_inframe_deletion+splice_region_variant+splice_region_variant+intron_variant_percent	frameshift_variant+stop_lost	frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant	sequence_feature_percent	intron_variant	frameshift_variant+splice_region_variant_percent	splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant	splice_donor_variant+5_prime_UTR_variant+intron_variant	Number_of_known_variants <br>(i.e. non-empty ID)_percent	start_lost+disruptive_inframe_insertion_percent	splice_acceptor_variant+splice_donor_variant+intron_variant	Transitions	DOWNSTREAM	SPLICE_SITE_DONOR_percent	frameshift_variant+stop_lost_percent	splice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent	splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent	EXON_percent	frameshift_variant_percent	Number_of_variants_before_filter	disruptive_inframe_insertion_percent	splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant_percent	splice_acceptor_variant+intron_variant	stop_gained+inframe_insertion	upstream_gene_variant_percent	SPLICE_SITE_ACCEPTOR	TF_binding_site_variant_percent	SPLICE_SITE_REGION	Genome_effective_length	frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant_percent	splice_acceptor_variant+5_prime_UTR_variant+intron_variant	INTERGENIC_percent	splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant	5_prime_UTR_variant	UPSTREAM_percent	splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant	splice_acceptor_variant+disruptive_inframe_deletion+splice_region_variant+splice_region_variant+intron_variant	splice_acceptor_variant+splice_region_variant+intron_variant	5_prime_UTR_variant_percent	Type	splice_acceptor_variant+inframe_deletion+splice_region_variant+splice_region_variant+intron_variant	Hom	splice_donor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant	splice_region_variant+splice_region_variant_percent	UTR_5_PRIME_percent	sequence_feature	intergenic_region_percent	transcript_percent	HIGH	frameshift_variant+splice_donor_variant+splice_region_variant+intron_variant	UPSTREAM	splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent	inframe_deletion+splice_region_variant_percent	transcript	splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent	Genome_total_length	Number_of_effects	NONE_percent	frameshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant	SPLICE_SITE_ACCEPTOR_percent	splice_acceptor_variant+intron_variant_percent	splice_donor_variant+intron_variant_percent	splice_donor_variant+5_prime_UTR_variant+intron_variant_percent	splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent	splice_acceptor_variant+splice_donor_variant+intron_variant_percent	splice_donor_variant+splice_region_variant+intron_variant	splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant_percent	Transversions	Genome	disruptive_inframe_deletion	MODIFIER	splice_acceptor_variant+splice_region_variant+intron_variant_percent	frameshift_variant+start_lost	SPLICE_SITE_REGION_percent	splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant	INTRON_percent	splice_acceptor_variant+5_prime_UTR_variant+intron_variant_percent	splice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant	TF_binding_site_variant	MOTIF_percent	frameshift_variant+splice_donor_variant+splice_region_variant+intron_variant_percent	inframe_insertion	splice_region_variant+intron_variant	stop_gained+inframe_insertion_percent	inframe_insertion+splice_region_variant	Number_of_known_variants <br>(i.e. non-empty ID)	splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant	3_prime_UTR_variant_percent	splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant	splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant_percent	downstream_gene_variant_percent	INTERGENIC	splice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant	splice_region_variant+splice_region_variant	splice_donor_variant+splice_region_variant+intron_variant_percent	splice_region_variant	splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant	splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant	splice_region_variant+intron_variant_percent	splice_region_variant_percent	SPLICE_SITE_DONOR	inframe_insertion_percent	intergenic_region	TRANSCRIPT_percent	intragenic_variant
snpeff	3322.0	1.8e-05	462.0	0.000109	1.0	1.0	1.8e-05	2174772.0	0.004855	0.0084	15811.0	1.8e-05	2.0	0.0	9.1e-05	3.6e-05	0.287478	10.0	2.0	0.007418	2126738.0	2178258.0	524875.0	1.0	1.8e-05	159.0	0.000127	15320.0	21.0	3.6e-05	6.178119	2.0	986.0	1.0	3.0	0.000382	17369.0	1.0	354347.0	38.668709	1.8e-05	0.002891	0.024855	15811.0	41.0	0.000145	277.0	0.278551	3190.0	3.6e-05	0.060401	1.8e-05	3352.0	1.0	800.0	339790.0	60.30929	1.8e-05	39.605454	77.0	?	0.0	3.6e-05	1.8e-05	3.0	2.0	39.535817	2126738.0	0.0014	13.0	2.0	78.616167	1.8e-05	61.0	0.0	339790.0	0.001473	5.5e-05	3.6e-05	9.1e-05	0.315806	0.014546	972155.0	0.005036	5.5e-05	224.0	3.0	6.442797	360.0	0.017928	5040.0	3101536026.0	3.6e-05	2.0	8.386471	5.0	3350.0	6.442797	12.0	1.0	32.0	0.06091	Count	1.0	392480.0	1.0	1.8e-05	0.060947	2174428.0	8.386471	0.0014	1367.0	3.0	354347.0	0.000236	0.000182	77.0	9.1e-05	32036512383.0	5499894.0	39.542071	6.0	0.006546	0.004073	0.000745	3.6e-05	0.000218	0.001109	15.0	1.8e-05	0.0	GRCh37.75	408.0	3316947.0	0.000582	8.0	0.091638	5.0	38.668709	3.6e-05	7.0	986.0	0.017928	5.5e-05	266.0	4390.0	5.5e-05	2.0	764271.0	5.0	0.287478	1.0	5.5e-05	6.178119	461247.0	2.0	1.0	0.000273	187.0	3.0	1.0	0.07982	0.0034	81.0	0.004836	461247.0	1.8e-05	267.0