# Summary table Name , Value Genome , GRCh38.105 Date , 2026-06-08 20:52 SnpEff_version , SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani Command_line_arguments , SnpEff GRCh38.105 -csvStats custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff.csv custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann.vcf.gz Warnings , 51 Number_of_lines_in_input_file, 88 Number_of_variants_before_filter, 88 Number_of_not_variants , 0 Number_of_variants_processed , 88 Number_of_known_variants (i.e. non-empty ID) , 0, 0% Number_of_effects , 129 Genome_total_length ,63147197748 Genome_effective_length ,46709983 Change_rate , 530795 # Change rate by chromosome Chromosome , Length , Changes , Change_rate 21 , 46709983 , 88 , 530795 # Variantss by type Type , Count , Percent DEL , 52 , 59.090909% INS , 36 , 40.909091% # Effects by impact Type , Count , Percent HIGH , 8 , 6.20155% LOW , 9 , 6.976744% MODERATE , 8 , 6.20155% MODIFIER , 104 , 80.620155% # Effects by functional class Type , Count , Percent Missense_Silent_ratio, 0 # Count by effects Type , Count , Percent 3_prime_UTR_variant , 2 , 1.449275% 5_prime_UTR_variant , 1 , 0.724638% conservative_inframe_deletion , 1 , 0.724638% disruptive_inframe_deletion , 3 , 2.173913% disruptive_inframe_insertion , 4 , 2.898551% downstream_gene_variant , 13 , 9.42029% frameshift_variant , 8 , 5.797101% intergenic_region , 1 , 0.724638% intragenic_variant , 5 , 3.623188% intron_variant , 75 , 54.347826% non_coding_transcript_exon_variant , 3 , 2.173913% splice_region_variant , 9 , 6.521739% upstream_gene_variant , 13 , 9.42029% # Count by genomic region Type , Count , Percent DOWNSTREAM , 13 , 10.077519% EXON , 19 , 14.728682% INTERGENIC , 1 , 0.775194% INTRON , 66 , 51.162791% SPLICE_SITE_REGION , 9 , 6.976744% TRANSCRIPT , 5 , 3.875969% UPSTREAM , 13 , 10.077519% UTR_3_PRIME , 2 , 1.550388% UTR_5_PRIME , 1 , 0.775194% # Quality # InDel lengths Values , 0,1,2 Count , 33,53,2 # Base changes base , A , C , G , T A , 0 , 0 , 0 , 0 C , 0 , 0 , 0 , 0 G , 0 , 0 , 0 , 0 T , 0 , 0 , 0 , 0 # Ts/Tv summary Transitions , 0 Transversions , 0 Ts_Tv_ratio , 0 # Ts/Tv : All variants No results available (empty input?) # Ts/Tv : Known variants No results available (empty input?) # Allele frequency # Allele frequency : All variants Values , 0 Count , 88 # Allele Count Values , 0 Count , 88 # Hom/Het table Sample_names , NORMAL, TUMOR Reference , 0, 0 Het , 0, 0 Hom , 0, 0 Missing , 88, 88 # Codon change table codons , - , AAA , AAC , ACA , ACC , AGG , CAA , CAG , CGC , CGG , CTG , GAA , GAG , GGA , TCA , TGC , TTC , TTT - , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 2 , 0 , 0 , 0 , 0 , 2 , 0 , 0 , 0 , 0 , 0 AAA , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 AAC , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ACA , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ACC , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 AGG , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 CAA , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 CAG , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 CGC , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 CGG , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 CTG , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 GAA , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 GAG , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 4 , 0 , 0 , 0 , 0 , 0 , 0 GGA , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 TCA , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 TGC , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 TTC , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 TTT , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 # Amino acid change table aa , - , ? , C , E , F , G , K , L , N , Q , R , S , T - , 0 , 4 , 0 , 2 , 0 , 0 , 0 , 0 , 0 , 2 , 0 , 0 , 0 ? , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 C , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 E , 2 , 0 , 0 , 4 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 F , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 G , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 K , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 L , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 1 , 0 , 0 N , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 Q , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 R , 2 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 S , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 T , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 # Chromosome change table 21, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000 21,Count,0,0,0,0,0,0,0,0,0,0,3,0,0,0,2,1,0,1,2,0,0,2,0,0,0,3,1,0,3,2,2,6,3,9,1,1,9,4,1,3,1,11,2,3,3,3,6