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 2026-02-02 21:39

SnpEff version
SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani

Command line arguments
SnpEff GRCh38.105 -csvStats Sig_18_Blood.mutect2_tumor_only.filtered_custom.ann_snpEff.csv Sig_18_Blood.mutect2_tumor_only.filtered_custom.ann.vcf.gz

Warnings 7

Errors 0

Number of lines (input file) 75

Number of variants (before filter) 94

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

Number of variants processed
(i.e. after filter and non-variants) 94

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

Number of multi-allelic VCF entries
(i.e. more than two alleles) 7

Number of effects 141

Genome total length 63,147,197,748

Genome effective length 46,709,983

Variant rate 1 variant every 496,914 bases

Variants rate details

Chromosome Length Variants Variants rate

21 46,709,983 94 496,914

Total 46,709,983 94 496,914

Chromosome	Length	Variants	Variants rate
21	46,709,983	94	496,914
Total	46,709,983	94	496,914

Number variants by type

Type Total

SNP 56

MNP 0

INS 16

DEL 22

MIXED 0

INV 0

DUP 0

BND 0

INTERVAL 0

Total 94

Type	Total
SNP	56
MNP	0
INS	16
DEL	22
MIXED	0
INV	0
DUP	0
BND	0
INTERVAL	0
Total	94

Number of effects by impact

Type (alphabetical order) Count Percent

HIGH 3 2.128%

LOW 12 8.511%

MODERATE 36 25.532%

MODIFIER 90 63.83%

Type (alphabetical order)	Count	Percent
HIGH	3	2.128%
LOW	12	8.511%
MODERATE	36	25.532%
MODIFIER	90	63.83%

Number of effects by functional class

Type (alphabetical order) Count Percent

MISSENSE 30 69.767%

NONSENSE 2 4.651%

SILENT 11 25.581%

Type (alphabetical order)	Count	Percent
MISSENSE	30	69.767%
NONSENSE	2	4.651%
SILENT	11	25.581%

Missense / Silent ratio: 2.7273

Number of effects by type and region

Type Region

Type (alphabetical order) Count Percent

3_prime_UTR_variant 6 4.196%

5_prime_UTR_variant 6 4.196%

conservative_inframe_deletion 1 0.699%

conservative_inframe_insertion 1 0.699%

disruptive_inframe_deletion 1 0.699%

disruptive_inframe_insertion 3 2.098%

downstream_gene_variant 14 9.79%

frameshift_variant 1 0.699%

intragenic_variant 8 5.594%

intron_variant 40 27.972%

missense_variant 30 20.979%

non_coding_transcript_exon_variant 5 3.497%

splice_region_variant 2 1.399%

stop_gained 2 1.399%

synonymous_variant 11 7.692%

upstream_gene_variant 12 8.392%

Type (alphabetical order) Count Percent

DOWNSTREAM 14 9.929%

EXON 54 38.298%

INTRON 40 28.369%

SPLICE_SITE_REGION 1 0.709%

TRANSCRIPT 8 5.674%

UPSTREAM 12 8.511%

UTR_3_PRIME 6 4.255%

UTR_5_PRIME 6 4.255%

Quality:

Insertions and deletions length:

	
		 Min 0  
		 Max 38  
		 Mean 2.079  
		 Median 1  
		 Standard deviation 6.064  
		 Values 0,1,2,3,4,5,38  
		 Count 6,27,1,1,1,1,1

Min	0
Max	38
Mean	2.079
Median	1
Standard deviation	6.064
Values	0,1,2,3,4,5,38
Count	6,27,1,1,1,1,1

Base changes (SNPs)

A C G T

A 0 3 11 3

C 5 0 2 6

G 7 1 0 6

T 2 7 3 0

	A	C	G	T
A	0	3	11	3
C	5	0	2	6
G	7	1	0	6
T	2	7	3	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	30
Transversions	25
Ts/Tv ratio	1.2

All variants:

Sample ,Sig_18_Sig_18_Blood,Total
Transitions ,30,30
Transversions ,25,25
Ts/Tv ,1.200,1.200

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

No results available (empty input?)

Allele frequency

Min	50
Max	250
Mean	62.667
Median	50
Standard deviation	42.786
Values	50,100,150,200,250
Count	68,1,2,2,2

Allele Count

Min	1
Max	5
Mean	1.253
Median	1
Standard deviation	0.856
Values	1,2,3,4,5
Count	68,1,2,2,2

Hom/Het per sample

Sample_names , Sig_18_Sig_18_Blood
Reference , 0
Het , 68
Hom , 1
Missing , 0

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 AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGT CTG GAA GAC GAG GCA GCC GCG GGA GGC GGG GGT GTC GTG GTT TAA TAC TAG TAT TCA TCC TCG TCT TGC TGT TTA TTC TTT

- 1 1 1 1 1 1 1 2 1 1 1 2 1 1 1

AAA 1

AAC

AAG 1 1

AAT 1 1 1

ACA 1

ACC 1 1

ACG

ACT 1 1

AGA 1

AGC 1

AGG

AGT

ATC 1

ATG

ATT 1

CAA

CAC 2

CAG 1

CAT

CCA 2

CCC 1

CCG 2

CCT 1

CGA

CGC 1 1

CGT 1

CTG 1

GAA

GAC 1 1

GAG 2 1

GCA 1

GCC

GCG 1 1 1

GGA 1

GGC 1 1

GGG

GGT

GTC

GTG

GTT 1

TAA

TAC 1 1

TAG

TAT 1 1

TCA 1

TCC 1 1

TCG 1

TCT 1

TGC 1

TGT

TTA 1

TTC 1

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 Y

*

- 1 3 1 1 1 1 1 2 1 1 1 2 1

A 1 1 1 1

C 1

D 1 1

E 2 1

F 1

G 1 2

H 2

I 1 1

K 1 1 1

L 1 1

M

N 1 1 1

P 2 1 2 1

Q 1

R 2 1 1

S 2 1 1 1 1

T 2 1 2

V 1

Y 1 1 2

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,0,0,0,0,0,0,0,0,0,0,8,0,0,0,1,1,0,1,1,0,0,0,0,0,0,0,1,0,1,0,7,0,2,3,8,5,1,1,2,3,0,27,2,1,13,3,2

Details by gene

Here you can find a tab-separated table.

Genome	GRCh38.105
Date	2026-02-02 21:39
SnpEff version	SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
Command line arguments	SnpEff GRCh38.105 -csvStats Sig_18_Blood.mutect2_tumor_only.filtered_custom.ann_snpEff.csv Sig_18_Blood.mutect2_tumor_only.filtered_custom.ann.vcf.gz
Warnings	7
Errors	0
Number of lines (input file)	75
Number of variants (before filter)	94
Number of not variants (i.e. reference equals alternative)	0
Number of variants processed (i.e. after filter and non-variants)	94
Number of known variants (i.e. non-empty ID)	0 ( 0% )
Number of multi-allelic VCF entries (i.e. more than two alleles)	7
Number of effects	141
Genome total length	63,147,197,748
Genome effective length	46,709,983
Variant rate	1 variant every 496,914 bases

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGC	AGG	AGT	ATG	CAA	CAC	CAG	CAT	CCA	CCC	CGA	CGT	CTG	GAA	GAC	GAG	GCA	GCC	GGG	GGT	GTC	GTG	GTT	TAA	TAC	TAG	TAT	TCA	TGC	TGT	TTC	TTT
-					1	1			1			1	1		1	1		2			1		1	1	2			1		1										1
AAA				1
AAC
AAG					1						1
AAT		1	1									1
ACA																										1
ACC																			1								1
ACG
ACT							1	1
AGA										1
AGC			1
AGG
AGT
ATC							1
ATG
ATT													1
CAA
CAC														2
CAG															1
CAT
CCA	2
CCC																		1
CCG																						2
CCT																	1
CGA
CGC															1					1
CGT																	1
CTG	1
GAA
GAC			1																				1
GAG																							2					1
GCA																							1
GCC
GCG								1																		1					1
GGA																													1
GGC	1																												1
GGG
GGT
GTC
GTG
GTT																																1
TAA
TAC																																				1		1
TAG
TAT																																		1							1
TCA																																	1
TCC																			1																			1
TCG																																			1
TCT																																				1
TGC																																							1
TGT
TTA																																					1
TTC	1
TTT

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

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGC	AGG	AGT	ATG	CAA	CAC	CAG	CAT	CCA	CCC	CGA	CGT	CTG	GAA	GAC	GAG	GCA	GCC	GGG	GGT	GTC	GTG	GTT	TAA	TAC	TAG	TAT	TCA	TGC	TGT	TTC	TTT
-					1	1			1			1	1		1	1		2			1		1	1	2			1		1										1
AAA				1
AAC
AAG					1						1
AAT		1	1									1
ACA																										1
ACC																			1								1
ACG
ACT							1	1
AGA										1
AGC			1
AGG
AGT
ATC							1
ATG
ATT													1
CAA
CAC														2
CAG															1
CAT
CCA	2
CCC																		1
CCG																						2
CCT																	1
CGA
CGC															1					1
CGT																	1
CTG	1
GAA
GAC			1																				1
GAG																							2					1
GCA																							1
GCC
GCG								1																		1					1
GGA																													1
GGC	1																												1
GGG
GGT
GTC
GTG
GTT																																1
TAA
TAC																																				1		1
TAG
TAT																																		1							1
TCA																																	1
TCC																			1																			1
TCG																																			1
TCT																																				1
TGC																																							1
TGT
TTA																																					1
TTC	1
TTT

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

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGC	AGG	AGT	ATG	CAA	CAC	CAG	CAT	CCA	CCC	CGA	CGT	CTG	GAA	GAC	GAG	GCA	GCC	GGG	GGT	GTC	GTG	GTT	TAA	TAC	TAG	TAT	TCA	TGC	TGT	TTC	TTT
-					1	1			1			1	1		1	1		2			1		1	1	2			1		1										1
AAA				1
AAC
AAG					1						1
AAT		1	1									1
ACA																										1
ACC																			1								1
ACG
ACT							1	1
AGA										1
AGC			1
AGG
AGT
ATC							1
ATG
ATT													1
CAA
CAC														2
CAG															1
CAT
CCA	2
CCC																		1
CCG																						2
CCT																	1
CGA
CGC															1					1
CGT																	1
CTG	1
GAA
GAC			1																				1
GAG																							2					1
GCA																							1
GCC
GCG								1																		1					1
GGA																													1
GGC	1																												1
GGG
GGT
GTC
GTG
GTT																																1
TAA
TAC																																				1		1
TAG
TAT																																		1							1
TCA																																	1
TCC																			1																			1
TCG																																			1
TCT																																				1
TGC																																							1
TGT
TTA																																					1
TTC	1
TTT

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