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 21:40

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.tiddit_sv_merge_custom.ann_snpEff.csv HCC1395_tumor_vs_HCC1395_BL.tiddit_sv_merge_custom.ann.vcf.gz

Warnings 0

Errors 0

Number of lines (input file) 4

Number of variants (before filter) 4

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

Number of variants processed
(i.e. after filter and non-variants) 4

Number of known variants
(i.e. non-empty ID) 3 ( 75% )

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

Number of effects 45

Genome total length 63,147,197,748

Genome effective length 46,709,983

Variant rate 1 variant every 11,677,495 bases

Variants rate details

Chromosome Length Variants Variants rate

21 46,709,983 4 11,677,495

Total 46,709,983 4 11,677,495

Chromosome	Length	Variants	Variants rate
21	46,709,983	4	11,677,495
Total	46,709,983	4	11,677,495

Number variants by type

Type Total

SNP 0

MNP 0

INS 0

DEL 1

MIXED 0

INV 0

DUP 2

BND 1

INTERVAL 0

Total 4

Type	Total
SNP	0
MNP	0
INS	0
DEL	1
MIXED	0
INV	0
DUP	2
BND	1
INTERVAL	0
Total	4

Number of effects by impact

Type (alphabetical order) Count Percent

HIGH 31 68.889%

MODIFIER 14 31.111%

Type (alphabetical order)		Count	Percent
HIGH		31	68.889%
MODIFIER		14	31.111%

Number of effects by functional class

Type (alphabetical order) Count Percent

Missense / Silent ratio: 0

Number of effects by type and region

Type Region

Type (alphabetical order) Count Percent

bidirectional_gene_fusion 1 1.887%

downstream_gene_variant 5 9.434%

exon_loss_variant 19 35.849%

feature_ablation 1 1.887%

frameshift_variant 5 9.434%

gene_fusion 5 9.434%

intragenic_variant 3 5.66%

intron_variant 2 3.774%

non_coding_transcript_exon_variant 1 1.887%

splice_donor_variant 1 1.887%

splice_region_variant 1 1.887%

stop_lost 1 1.887%

transcript_ablation 3 5.66%

upstream_gene_variant 5 9.434%

Type (alphabetical order) Count Percent

DOWNSTREAM 5 11.111%

EXON 20 44.444%

GENE 7 15.556%

INTRON 1 2.222%

SPLICE_SITE_DONOR 1 2.222%

TRANSCRIPT 6 13.333%

UPSTREAM 5 11.111%

Quality:

	
		 Min 50  
		 Max 80  
		 Mean 72.5  
		 Median 80  
		 Standard deviation 15  
		 Values 50,80  
		 Count 1,3

Insertions and deletions length:

	
		 Min 1  
		 Max 1  
		 Mean 1  
		 Median 0.5  
		 Standard deviation 0  
		 Values 1  
		 Count 1

Base changes (SNPs)

A C G T

A 0 0 0 0

C 0 0 0 0

G 0 0 0 0

T 0 0 0 0

	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 (transitions / transversions)

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

Transitions	0
Transversions	0
Ts/Tv ratio	0

All variants:

No results available (empty input?)

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

No results available (empty input?)

Allele frequency

Min	50
Max	100
Mean	87.5
Median	100
Standard deviation	25
Values	50,100
Count	1,3

Allele Count

Min	1
Max	2
Mean	1.75
Median	2
Standard deviation	0.5
Values	1,2
Count	1,3

Hom/Het per sample

Sample_names , HCC1395_HCC1395_BL, HCC1395_HCC1395_tumor
Reference , 0, 0
Het , 1, 0
Hom , 2, 1
Missing , 1, 3

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 ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAC TAT TCA TCC TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT

-

AAA 10

AAC 10

AAG 17

AAT 3

ACA 3

ACC 18

ACG 6

ACT 4

AGA 2

AGC 21

AGG 10

AGT 7

ATA 3

ATC 10

ATG 11

ATT 3

CAA 5

CAC 22

CAG 20

CAT 5

CCA 10

CCC 24

CCG 15

CCT 8

CGA 1

CGC 11

CGG 8

CTA 2

CTC 9

CTG 41

CTT 4

GAA 10

GAC 14

GAG 21

GAT 4

GCA 6

GCC 32

GCG 17

GCT 8

GGA 9

GGC 23

GGG 7

GGT 2

GTA 2

GTC 10

GTG 23

GTT 1

TAC 24

TAT 6

TCA 2

TCC 16

TCG 7

TCT 6

TGA 1

TGC 11

TGG 6

TGT 2

TTA 4

TTC 15

TTG 7

TTT 4

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

* 1

-

?

A 63

C 13

D 18

E 31

F 19

G 41

H 27

I 16

K 27

L 67

M 11

N 13

P 57

Q 25

R 32

S 59

T 30 1

V 36

W 6

Y 30

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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,1,0,0,0

Details by gene

Here you can find a tab-separated table.

Genome	GRCh38.105
Date	2026-02-02 21:40
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.tiddit_sv_merge_custom.ann_snpEff.csv HCC1395_tumor_vs_HCC1395_BL.tiddit_sv_merge_custom.ann.vcf.gz
Warnings	0
Errors	0
Number of lines (input file)	4
Number of variants (before filter)	4
Number of not variants (i.e. reference equals alternative)	0
Number of variants processed (i.e. after filter and non-variants)	4
Number of known variants (i.e. non-empty ID)	3 ( 75% )
Number of multi-allelic VCF entries (i.e. more than two alleles)	0
Number of effects	45
Genome total length	63,147,197,748
Genome effective length	46,709,983
Variant rate	1 variant every 11,677,495 bases

Min	50
Max	80
Mean	72.5
Median	80
Standard deviation	15
Values	50,80
Count	1,3

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGA	AGC	AGG	AGT	ATA	ATC	ATG	ATT	CAA	CAC	CAG	CAT	CCA	CCC	CCG	CCT	CGA	CGC	CGG	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCG	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	GTT	TAC	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	10
AAC	10
AAG	17
AAT	3
ACA	3
ACC	18
ACG	6
ACT	4
AGA	2
AGC	21
AGG	10
AGT	7
ATA	3
ATC	10
ATG	11
ATT	3
CAA	5
CAC	22
CAG	20
CAT	5
CCA	10
CCC	24
CCG	15
CCT	8
CGA	1
CGC	11
CGG	8
CTA	2
CTC	9
CTG	41
CTT	4
GAA	10
GAC	14
GAG	21
GAT	4
GCA	6
GCC	32
GCG	17
GCT	8
GGA	9
GGC	23
GGG	7
GGT	2
GTA	2
GTC	10
GTG	23
GTT	1
TAC	24
TAT	6
TCA	2
TCC	16
TCG	7
TCT	6
TGA	1
TGC	11
TGG	6
TGT	2
TTA	4
TTC	15
TTG	7
TTT	4

	-	?
*	1
-
?
A	63
C	13
D	18
E	31
F	19
G	41
H	27
I	16
K	27
L	67
M	11
N	13
P	57
Q	25
R	32
S	59
T	30	1
V	36
W	6
Y	30

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGA	AGC	AGG	AGT	ATA	ATC	ATG	ATT	CAA	CAC	CAG	CAT	CCA	CCC	CCG	CCT	CGA	CGC	CGG	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCG	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	GTT	TAC	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	10
AAC	10
AAG	17
AAT	3
ACA	3
ACC	18
ACG	6
ACT	4
AGA	2
AGC	21
AGG	10
AGT	7
ATA	3
ATC	10
ATG	11
ATT	3
CAA	5
CAC	22
CAG	20
CAT	5
CCA	10
CCC	24
CCG	15
CCT	8
CGA	1
CGC	11
CGG	8
CTA	2
CTC	9
CTG	41
CTT	4
GAA	10
GAC	14
GAG	21
GAT	4
GCA	6
GCC	32
GCG	17
GCT	8
GGA	9
GGC	23
GGG	7
GGT	2
GTA	2
GTC	10
GTG	23
GTT	1
TAC	24
TAT	6
TCA	2
TCC	16
TCG	7
TCT	6
TGA	1
TGC	11
TGG	6
TGT	2
TTA	4
TTC	15
TTG	7
TTT	4

	-	?
*	1
-
?
A	63
C	13
D	18
E	31
F	19
G	41
H	27
I	16
K	27
L	67
M	11
N	13
P	57
Q	25
R	32
S	59
T	30	1
V	36
W	6
Y	30

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGA	AGC	AGG	AGT	ATA	ATC	ATG	ATT	CAA	CAC	CAG	CAT	CCA	CCC	CCG	CCT	CGA	CGC	CGG	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCG	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	GTT	TAC	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	10
AAC	10
AAG	17
AAT	3
ACA	3
ACC	18
ACG	6
ACT	4
AGA	2
AGC	21
AGG	10
AGT	7
ATA	3
ATC	10
ATG	11
ATT	3
CAA	5
CAC	22
CAG	20
CAT	5
CCA	10
CCC	24
CCG	15
CCT	8
CGA	1
CGC	11
CGG	8
CTA	2
CTC	9
CTG	41
CTT	4
GAA	10
GAC	14
GAG	21
GAT	4
GCA	6
GCC	32
GCG	17
GCT	8
GGA	9
GGC	23
GGG	7
GGT	2
GTA	2
GTC	10
GTG	23
GTT	1
TAC	24
TAT	6
TCA	2
TCC	16
TCG	7
TCT	6
TGA	1
TGC	11
TGG	6
TGT	2
TTA	4
TTC	15
TTG	7
TTT	4

	-	?
*	1
-
?
A	63
C	13
D	18
E	31
F	19
G	41
H	27
I	16
K	27
L	67
M	11
N	13
P	57
Q	25
R	32
S	59
T	30	1
V	36
W	6
Y	30