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HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.csv
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s3://natera-rnd-pltf-dev-s3-gitlab-results/sarek/build2800220/baseline-run/63640739/reports/raw_qc/snpeff/strelka/HCC1395_tumor_vs_HCC1395_BL/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.csv
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gitlab-sarek-build2800220-baseline-run-63640739
Published
Jun 05, 2026 8:27 AM

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# 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
156 rows