SnpEff: Variant analysis

Contents Summary
Variant rate by chromosome
Variants by type
Number of variants by impact
Number of variants by functional class
Number of variants by effect
Quality histogram
InDel length histogram
Base variant table
Transition vs transversions (ts/tv)
Allele frequency
Allele Count
Codon change table
Amino acid change table
Chromosome variants plots
Details by gene

Summary

Genome GRCh38.105

Date 2026-06-05 00:06

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_snvs_custom.ann_snpEff.csv custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann.vcf.gz

Warnings 7

Errors 0

Number of lines (input file) 237

Number of variants (before filter) 237

Number of not variants
(i.e. reference equals alternative) 0

Number of variants processed
(i.e. after filter and non-variants) 237

Number of known variants
(i.e. non-empty ID) 0 ( 0% )

Number of multi-allelic VCF entries
(i.e. more than two alleles) 0

Number of effects 381

Genome total length 63,147,197,748

Genome effective length 46,709,983

Variant rate 1 variant every 197,088 bases

Variants rate details

Chromosome Length Variants Variants rate

21 46,709,983 237 197,088

Total 46,709,983 237 197,088

Chromosome	Length	Variants	Variants rate
21	46,709,983	237	197,088
Total	46,709,983	237	197,088

Number variants by type

Type Total

SNP 237

MNP 0

INS 0

DEL 0

MIXED 0

INV 0

DUP 0

BND 0

INTERVAL 0

Total 237

Type	Total
SNP	237
MNP	0
INS	0
DEL	0
MIXED	0
INV	0
DUP	0
BND	0
INTERVAL	0
Total	237

Number of effects by impact

Type (alphabetical order) Count Percent

HIGH 2 0.525%

LOW 34 8.924%

MODERATE 52 13.648%

MODIFIER 293 76.903%

Type (alphabetical order)	Count	Percent
HIGH	2	0.525%
LOW	34	8.924%
MODERATE	52	13.648%
MODIFIER	293	76.903%

Number of effects by functional class

Type (alphabetical order) Count Percent

MISSENSE 52 66.667%

NONSENSE 2 2.564%

SILENT 24 30.769%

Type (alphabetical order)	Count	Percent
MISSENSE	52	66.667%
NONSENSE	2	2.564%
SILENT	24	30.769%

Missense / Silent ratio: 2.1667

Number of effects by type and region

Type Region

Type (alphabetical order) Count Percent

3_prime_UTR_variant 9 2.29%

5_prime_UTR_premature_start_codon_gain_variant 1 0.254%

5_prime_UTR_variant 4 1.018%

downstream_gene_variant 33 8.397%

intergenic_region 1 0.254%

intragenic_variant 22 5.598%

intron_variant 189 48.092%

missense_variant 52 13.232%

non_coding_transcript_exon_variant 5 1.272%

splice_region_variant 12 3.053%

stop_gained 2 0.509%

synonymous_variant 24 6.107%

upstream_gene_variant 39 9.924%

Type (alphabetical order) Count Percent

DOWNSTREAM 33 8.661%

EXON 83 21.785%

INTERGENIC 1 0.262%

INTRON 180 47.244%

SPLICE_SITE_REGION 9 2.362%

TRANSCRIPT 22 5.774%

UPSTREAM 39 10.236%

UTR_3_PRIME 9 2.362%

UTR_5_PRIME 5 1.312%

Quality:

Insertions and deletions length:

Base changes (SNPs)

A C G T

A 0 10 16 4

C 32 0 11 46

G 43 8 0 18

T 5 26 18 0

	A	C	G	T
A	0	10	16	4
C	32	0	11	46
G	43	8	0	18
T	5	26	18	0

Ts/Tv (transitions / transversions)

Note: Only SNPs are used for this statistic.
Note: This Ts/Tv ratio is a 'raw' ratio (ratio of observed events).

Transitions	262
Transversions	212
Ts/Tv ratio	1.2358

All variants:

Sample ,NORMAL,TUMOR,Total
Transitions ,131,131,262
Transversions ,106,106,212
Ts/Tv ,1.236,1.236,1.236

Only known variants (i.e. the ones having a non-empty ID field):

No results available (empty input?)

Allele frequency

Min	0
Max	0
Mean	0
Median	0
Standard deviation	0
Values	0
Count	237

Allele Count

Min	0
Max	0
Mean	0
Median	0
Standard deviation	0
Values	0
Count	237

Hom/Het per sample

Sample_names , NORMAL, TUMOR
Reference , 0, 0
Het , 0, 0
Hom , 0, 0
Missing , 237, 237

Codon changes

How to read this table:
- Rows are reference codons and columns are changed codons. E.g. Row 'AAA' column 'TAA' indicates how many 'AAA' codons have been replaced by 'TAA' codons.
- Red background colors indicate that more changes happened (heat-map).
- Diagonals are indicated using grey background color
- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).

AAA AAC AAT ACA ACC ACG ACT AGA AGC AGT ATA ATC ATG ATT CAC CAG CAT CCA CCC CCG CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG TAC TAG TAT TCA TCC TCG TCT TGC TGG TGT TTA TTC TTT

AAA

AAC

AAT 1

ACA 1

ACC

ACG 2

ACT 1 1 1

AGA 1

AGC 1

AGT 1 1

ATA 1

ATC 2

ATG 1 1 1 1

ATT

CAC

CAG 1 1 1

CAT

CCA 1 1 1

CCC 1 1 1 1

CCG 2 1 1 4

CGA

CGC 1

CGG 1 1

CGT 1

CTA

CTC 1 1

CTG 1 1

CTT 1

GAA 1

GAC 1

GAG 4

GAT 1 1 1

GCC 1 1

GCG 1

GCT 1

GGA 1

GGC 1

GGG 2

GGT 2

GTA 1 1

GTC 1

GTG 1

TAC 1

TAG

TAT

TCA 1

TCC 2 1 1

TCG

TCT 1

TGC 1 1

TGG

TGT

TTA 1

TTC

TTT

Amino acid changes

How to read this table:
- Rows are reference amino acids and columns are changed amino acids. E.g. Row 'A' column 'E' indicates how many 'A' amino acids have been replaced by 'E' amino acids.
- Red background colors indicate that more changes happened (heat-map).
- Diagonals are indicated using grey background color
- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).

* A C D E F G H I K L M N P Q R S T V W Y

*

A 1 1 1 1

C 1 1

D 1 2 1

E 4 1

F

G 3 1 2

H

I 3

K

L 1 1 2 1 1

M 2 1 1

N 1

P 1 1 4 2 6 1

Q 1 1 1

R 1 1 1 1 1

S 1 1 1 1 1 2 1 1

T 1 1 1 3

V 1 3

W

Y 1

Variants by chromosome

		

		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,0,0,0,0,0,0,1,0,0,0,11,0,0,0,4,2,0,0,5,0,0,2,0,0,0,9,3,0,2,3,0,6,8,15,9,0,20,4,4,9,5,22,17,8,39,9,20

Details by gene

Here you can find a tab-separated table.

Genome	GRCh38.105
Date	2026-06-05 00:06
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_snvs_custom.ann_snpEff.csv custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann.vcf.gz
Warnings	7
Errors	0
Number of lines (input file)	237
Number of variants (before filter)	237
Number of not variants (i.e. reference equals alternative)	0
Number of variants processed (i.e. after filter and non-variants)	237
Number of known variants (i.e. non-empty ID)	0 ( 0% )
Number of multi-allelic VCF entries (i.e. more than two alleles)	0
Number of effects	381
Genome total length	63,147,197,748
Genome effective length	46,709,983
Variant rate	1 variant every 197,088 bases

	AAA	AAC	AAT	ACA	ACC	ACG	AGA	AGC	ATA	ATC	ATG	ATT	CAC	CAG	CAT	CCA	CCC	CCG	CGA	CTA	CTC	GAA	GAC	GAT	GCC	GCT	GGC	GGT	GTA	GTC	GTG	TAC	TAG	TAT	TCA	TCC	TCG	TGC	TGG	TGT	TTC	TTT
AAA
AAC
AAT		1
ACA						1
ACC
ACG				2
ACT			1									1														1
AGA								1
AGC		1
AGT												1																1
ATA				1
ATC					2
ATG						1			1	1																					1
ATT
CAC
CAG													1					1															1
CAT
CCA																	1	1																	1
CCC					1								1								1															1
CCG														2		1	1																				4
CGA
CGC																																						1
CGG														1					1
CGT															1
CTA
CTC																	1																								1
CTG											1									1
CTT												1
GAA	1
GAC																						1
GAG																						4
GAT																						1	1											1
GCC					1																						1
GCG																															1
GCT																								1
GGA							1
GGC																												1
GGG																																							2
GGT																											2
GTA																														1	1
GTC										1
GTG																													1
TAC																																	1
TAG
TAT
TCA																																					1
TCC																	2								1							1
TCG
TCT																																										1
TGC																																				1				1
TGG
TGT
TTA																				1
TTC
TTT

	*	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*
A				1			1											1	1
C			1														1
D				1	2																1
E					4					1
F
G							3									1				2
H
I																		3
K
L						1			1		2	1		1
M									2									1	1
N													1
P								1			1			4	2		6	1
Q	1							1						1
R			1					1							1	1	1
S		1				1	1		1				1	2			1				1
T		1							1				1					3
V									1										3
W
Y	1

	AAA	AAC	AAT	ACA	ACC	ACG	AGA	AGC	ATA	ATC	ATG	ATT	CAC	CAG	CAT	CCA	CCC	CCG	CGA	CTA	CTC	GAA	GAC	GAT	GCC	GCT	GGC	GGT	GTA	GTC	GTG	TAC	TAG	TAT	TCA	TCC	TCG	TGC	TGG	TGT	TTC	TTT
AAA
AAC
AAT		1
ACA						1
ACC
ACG				2
ACT			1									1														1
AGA								1
AGC		1
AGT												1																1
ATA				1
ATC					2
ATG						1			1	1																					1
ATT
CAC
CAG													1					1															1
CAT
CCA																	1	1																	1
CCC					1								1								1															1
CCG														2		1	1																				4
CGA
CGC																																						1
CGG														1					1
CGT															1
CTA
CTC																	1																								1
CTG											1									1
CTT												1
GAA	1
GAC																						1
GAG																						4
GAT																						1	1											1
GCC					1																						1
GCG																															1
GCT																								1
GGA							1
GGC																												1
GGG																																							2
GGT																											2
GTA																														1	1
GTC										1
GTG																													1
TAC																																	1
TAG
TAT
TCA																																					1
TCC																	2								1							1
TCG
TCT																																										1
TGC																																				1				1
TGG
TGT
TTA																				1
TTC
TTT

	*	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*
A				1			1											1	1
C			1														1
D				1	2																1
E					4					1
F
G							3									1				2
H
I																		3
K
L						1			1		2	1		1
M									2									1	1
N													1
P								1			1			4	2		6	1
Q	1							1						1
R			1					1							1	1	1
S		1				1	1		1				1	2			1				1
T		1							1				1					3
V									1										3
W
Y	1

	AAA	AAC	AAT	ACA	ACC	ACG	AGA	AGC	ATA	ATC	ATG	ATT	CAC	CAG	CAT	CCA	CCC	CCG	CGA	CTA	CTC	GAA	GAC	GAT	GCC	GCT	GGC	GGT	GTA	GTC	GTG	TAC	TAG	TAT	TCA	TCC	TCG	TGC	TGG	TGT	TTC	TTT
AAA
AAC
AAT		1
ACA						1
ACC
ACG				2
ACT			1									1														1
AGA								1
AGC		1
AGT												1																1
ATA				1
ATC					2
ATG						1			1	1																					1
ATT
CAC
CAG													1					1															1
CAT
CCA																	1	1																	1
CCC					1								1								1															1
CCG														2		1	1																				4
CGA
CGC																																						1
CGG														1					1
CGT															1
CTA
CTC																	1																								1
CTG											1									1
CTT												1
GAA	1
GAC																						1
GAG																						4
GAT																						1	1											1
GCC					1																						1
GCG																															1
GCT																								1
GGA							1
GGC																												1
GGG																																							2
GGT																											2
GTA																														1	1
GTC										1
GTG																													1
TAC																																	1
TAG
TAT
TCA																																					1
TCC																	2								1							1
TCG
TCT																																										1
TGC																																				1				1
TGG
TGT
TTA																				1
TTC
TTT

	*	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*
A				1			1											1	1
C			1														1
D				1	2																1
E					4					1
F
G							3									1				2
H
I																		3
K
L						1			1		2	1		1
M									2									1	1
N													1
P								1			1			4	2		6	1
Q	1							1						1
R			1					1							1	1	1
S		1				1	1		1				1	2			1				1
T		1							1				1					3
V									1										3
W
Y	1