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custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff.csv
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s3://natera-rnd-pltf-dev-s3-gitlab-results/sarek/build2810611/regression-run/63904030/reports/raw_qc/snpeff/strelka/custom_Sig_18_tumor_normal/custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff.csv
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gitlab-sarek-build2810611-regression-run-63904030
Published
Jun 08, 2026 1:42 PM

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# Summary table
Name , Value
Genome , GRCh38.105
Date , 2026-06-08 20:42
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
167 rows