# Summary table Name , Value Genome , GRCh38.105 Date , 2026-06-05 15:26 SnpEff_version , SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani Command_line_arguments , SnpEff GRCh38.105 -csvStats HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.csv HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann.vcf.gz Warnings , 21 Number_of_lines_in_input_file, 42 Number_of_variants_before_filter, 42 Number_of_not_variants , 0 Number_of_variants_processed , 42 Number_of_known_variants (i.e. non-empty ID) , 0, 0% Number_of_effects , 65 Genome_total_length ,63147197748 Genome_effective_length ,46709983 Change_rate , 1112142 # Change rate by chromosome Chromosome , Length , Changes , Change_rate 21 , 46709983 , 42 , 1112142 # Variantss by type Type , Count , Percent DEL , 23 , 54.761905% INS , 19 , 45.238095% # Effects by impact Type , Count , Percent LOW , 5 , 7.692308% MODERATE , 6 , 9.230769% MODIFIER , 54 , 83.076923% # Effects by functional class Type , Count , Percent Missense_Silent_ratio, 0 # Count by effects Type , Count , Percent 3_prime_UTR_variant , 2 , 2.857143% 5_prime_UTR_variant , 1 , 1.428571% conservative_inframe_deletion , 1 , 1.428571% disruptive_inframe_deletion , 4 , 5.714286% disruptive_inframe_insertion , 1 , 1.428571% downstream_gene_variant , 8 , 11.428571% intragenic_variant , 3 , 4.285714% intron_variant , 37 , 52.857143% non_coding_transcript_exon_variant , 1 , 1.428571% non_coding_transcript_variant , 1 , 1.428571% splice_region_variant , 5 , 7.142857% upstream_gene_variant , 6 , 8.571429% # Count by genomic region Type , Count , Percent DOWNSTREAM , 8 , 12.307692% EXON , 7 , 10.769231% INTRON , 32 , 49.230769% SPLICE_SITE_REGION , 5 , 7.692308% TRANSCRIPT , 4 , 6.153846% UPSTREAM , 6 , 9.230769% UTR_3_PRIME , 2 , 3.076923% UTR_5_PRIME , 1 , 1.538462% # Quality # InDel lengths Values , 0,1,2,3 Count , 17,23,1,1 # 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 , 42 # Allele Count Values , 0 Count , 42 # Hom/Het table Sample_names , NORMAL, TUMOR Reference , 0, 0 Het , 0, 0 Hom , 0, 0 Missing , 42, 42 # Codon change table codons , - , ACA , ACC , CAC , CAT , CCA , CCC , CCG , CTA , GAG , GCC , GCG , GCT , GGC , GGG - , 0 , 0 , 0 , 0 , 1 , 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 ACC , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 CAC , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 CAT , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 CCA , 2 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 CCC , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 CCG , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 CTA , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 GAG , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 GCC , 2 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 GCG , 2 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 GCT , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 GGC , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 GGG , 3 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 # Amino acid change table aa , - , A , E , G , H , L , P , T - , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 A , 5 , 1 , 0 , 0 , 0 , 0 , 0 , 0 E , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 G , 4 , 0 , 0 , 0 , 0 , 0 , 0 , 0 H , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 L , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 P , 3 , 0 , 0 , 0 , 0 , 0 , 1 , 0 T , 1 , 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,0,0,0,0,0,0,0,0,0,0,2,0,0,0,1,2,0,0,0,0,0,2,0,0,0,1,1,0,2,1,0,0,1,2,3,0,4,1,0,1,1,3,0,1,2,3,8