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 2026-06-04 19:30

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.tnseq.filtered_snpEff.csv HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered.vcf.gz

Warnings 99

Errors 0

Number of lines (input file) 287

Number of variants (before filter) 398

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

Number of variants processed
(i.e. after filter and non-variants) 398

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

Number of multi-allelic VCF entries
(i.e. more than two alleles) 42

Number of effects 599

Genome total length 63,147,197,748

Genome effective length 46,709,983

Variant rate 1 variant every 117,361 bases

Variants rate details

Chromosome Length Variants Variants rate

21 46,709,983 398 117,361

Total 46,709,983 398 117,361

Chromosome	Length	Variants	Variants rate
21	46,709,983	398	117,361
Total	46,709,983	398	117,361

Number variants by type

Type Total

SNP 167

MNP 8

INS 95

DEL 128

MIXED 0

INV 0

DUP 0

BND 0

INTERVAL 0

Total 398

Type	Total
SNP	167
MNP	8
INS	95
DEL	128
MIXED	0
INV	0
DUP	0
BND	0
INTERVAL	0
Total	398

Number of effects by impact

Type (alphabetical order) Count Percent

HIGH 6 1.002%

LOW 28 4.674%

MODERATE 45 7.513%

MODIFIER 520 86.811%

Type (alphabetical order)	Count	Percent
HIGH	6	1.002%
LOW	28	4.674%
MODERATE	45	7.513%
MODIFIER	520	86.811%

Number of effects by functional class

Type (alphabetical order) Count Percent

MISSENSE 32 66.667%

NONSENSE 1 2.083%

SILENT 15 31.25%

Type (alphabetical order)	Count	Percent
MISSENSE	32	66.667%
NONSENSE	1	2.083%
SILENT	15	31.25%

Missense / Silent ratio: 2.1333

Number of effects by type and region

Type Region

Type (alphabetical order) Count Percent

3_prime_UTR_variant 7 1.138%

5_prime_UTR_variant 11 1.789%

conservative_inframe_deletion 4 0.65%

conservative_inframe_insertion 2 0.325%

disruptive_inframe_deletion 2 0.325%

disruptive_inframe_insertion 2 0.325%

downstream_gene_variant 52 8.455%

frameshift_variant 3 0.488%

intergenic_region 1 0.163%

intragenic_variant 30 4.878%

intron_variant 343 55.772%

missense_variant 35 5.691%

non_coding_transcript_exon_variant 14 2.276%

splice_acceptor_variant 1 0.163%

splice_region_variant 15 2.439%

stop_gained 1 0.163%

stop_lost 1 0.163%

synonymous_variant 15 2.439%

upstream_gene_variant 76 12.358%

Type (alphabetical order) Count Percent

DOWNSTREAM 52 8.681%

EXON 76 12.688%

INTERGENIC 1 0.167%

INTRON 331 55.259%

SPLICE_SITE_ACCEPTOR 1 0.167%

SPLICE_SITE_REGION 14 2.337%

TRANSCRIPT 30 5.008%

UPSTREAM 76 12.688%

UTR_3_PRIME 7 1.169%

UTR_5_PRIME 11 1.836%

Quality:

Insertions and deletions length:

	
		 Min 0  
		 Max 18  
		 Mean 1.578  
		 Median 1  
		 Standard deviation 2.638  
		 Values 0,1,2,3,4,5,6,7,9,11,12,13,17,18  
		 Count 47,143,8,5,1,4,1,4,3,3,1,1,1,1

Min	0
Max	18
Mean	1.578
Median	1
Standard deviation	2.638
Values	0,1,2,3,4,5,6,7,9,11,12,13,17,18
Count	47,143,8,5,1,4,1,4,3,3,1,1,1,1

Base changes (SNPs)

A C G T

A 0 6 30 4

C 14 0 8 27

G 25 12 0 13

T 5 18 5 0

	A	C	G	T
A	0	6	30	4
C	14	0	8	27
G	25	12	0	13
T	5	18	5	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	99
Transversions	65
Ts/Tv ratio	1.5231

All variants:

Sample ,HCC1395_BL,HCC1395_tumor,Total
Transitions ,0,99,99
Transversions ,0,65,65
Ts/Tv ,NaN,1.523,1.523

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

No results available (empty input?)

Allele frequency

Min	25
Max	275
Mean	34.669
Median	25
Standard deviation	30.298
Values	25,50,75,100,125,150,175,200,275
Count	245,17,8,6,4,3,2,1,1

Allele Count

Min	1
Max	11
Mean	1.387
Median	1
Standard deviation	1.212
Values	1,2,3,4,5,6,7,8,11
Count	245,17,8,6,4,3,2,1,1

Hom/Het per sample

Sample_names , HCC1395_BL, HCC1395_tumor
Reference , 287, 0
Het , 0, 245
Hom , 0, 17
Missing , 0, 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).

- AAC AAT ACA ACC ACT AGA AGC AGT ATA ATC ATG CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CTA CTC CTG GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TCA TCC TCG TCT TGC TGT TTA TTC TTG TTT

- 1 1 1 2

AAC 1

AAT 1

ACA

ACC 2 1

ACT

AGA 1

AGC 6 1

AGT 1

ATA 1

ATC 1

ATG

CAA 1

CAC 1 1 3 2

CAG

CAT 1 1

CCA

CCC 1 2

CCG 6 1 1

CCT 2

CGA 1

CGC

CGG 3

CTA 1 1 1

CTC 1

CTG 2 1

GAA 5

GAC 12 2

GAG 6 1 3

GAT 1 1 1

GCA 1

GCC 3 1

GCG 13 1 1

GCT 1

GGA 1

GGC 7 1

GGG 11 1

GGT 1

GTA 7 1

GTC 1 1 1

GTG 2 2

GTT 1

TAA

TAC 1

TAG 1

TCA

TCC 1 1 1

TCG 1

TCT 1

TGC

TGT 2

TTA 1

TTC 1

TTG

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 L M N P Q R S T V Y

* 1

- 1 2 1 1 1

?

A 17 2 1 1

C 2

D 13 2 2

E 11 3 1

F 1

G 19 2 1

H 1 4 1 1 2

I 1 1

L 3 1 1 2 1

M

N 1 1

P 6 1 2 1 1 2

Q 1

R 3 1 1

S 7 1 1 1 1 1 1

T 1 2

V 10 1 2 3

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,0,0,0,0,0,1,2,0,0,0,32,0,0,0,2,2,0,0,6,0,0,2,0,0,0,4,1,0,5,3,5,7,10,30,13,5,13,15,1,27,1,83,5,8,39,35,41

Details by gene

Here you can find a tab-separated table.

Genome	GRCh38.105
Date	2026-06-04 19:30
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.tnseq.filtered_snpEff.csv HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered.vcf.gz
Warnings	99
Errors	0
Number of lines (input file)	287
Number of variants (before filter)	398
Number of not variants (i.e. reference equals alternative)	0
Number of variants processed (i.e. after filter and non-variants)	398
Number of known variants (i.e. non-empty ID)	0 ( 0% )
Number of multi-allelic VCF entries (i.e. more than two alleles)	42
Number of effects	599
Genome total length	63,147,197,748
Genome effective length	46,709,983
Variant rate	1 variant every 117,361 bases

	-	AAC	AAT	ACA	ACT	AGC	AGT	ATA	ATC	ATG	CAC	CAG	CAT	CCA	CCC	CCG	CCT	CGC	CGG	CTC	CTG	GAA	GAC	GAG	GAT	GCC	GCT	GGA	GGC	GGT	GTA	GTC	GTG	GTT	TAA	TAC	TCA	TCC	TCG	TGC	TTG	TTT
-			1		1						1													2
AAC	1
AAT							1
ACA
ACC		2							1
ACT
AGA				1
AGC	6																												1
AGT						1
ATA	1
ATC																																1
ATG
CAA												1
CAC		1									1		3					2
CAG
CAT	1																1
CCA
CCC																										1												2
CCG	6																		1		1
CCT																														2
CGA														1
CGC
CGG	3
CTA	1							1												1
CTC															1
CTG	2															1
GAA	5
GAC	12																					2
GAG	6											1										3
GAT	1																						1		1
GCA																						1
GCC	3																										1
GCG	13									1																1
GCT	1
GGA																														1
GGC	7					1
GGG	11																											1
GGT	1
GTA	7																																1
GTC	1								1																						1
GTG	2									2
GTT																																		1
TAA
TAC																																			1
TAG																																							1
TCA
TCC	1																	1																		1
TCG																																									1
TCT																																										1
TGC
TGT																																								2
TTA																																					1
TTC	1
TTG
TTT

	*	-	?	A	C	D	E	F	G	H	I	L	M	N	P	Q	R	S	T	V	Y
*																		1
-			1				2			1				1					1
?
A		17		2			1						1
C					2
D		13				2	2
E		11					3									1
F		1
G		19							2									1
H		1								4				1	1		2
I		1																		1
L		3									1	1			2			1
M
N		1																1
P		6		1					2			1					1	2
Q																1
R		3													1				1
S		7						1	1			1					1	1			1
T											1			2
V		10									1		2							3
Y	1

	-	AAC	AAT	ACA	ACT	AGC	AGT	ATA	ATC	ATG	CAC	CAG	CAT	CCA	CCC	CCG	CCT	CGC	CGG	CTC	CTG	GAA	GAC	GAG	GAT	GCC	GCT	GGA	GGC	GGT	GTA	GTC	GTG	GTT	TAA	TAC	TCA	TCC	TCG	TGC	TTG	TTT
-			1		1						1													2
AAC	1
AAT							1
ACA
ACC		2							1
ACT
AGA				1
AGC	6																												1
AGT						1
ATA	1
ATC																																1
ATG
CAA												1
CAC		1									1		3					2
CAG
CAT	1																1
CCA
CCC																										1												2
CCG	6																		1		1
CCT																														2
CGA														1
CGC
CGG	3
CTA	1							1												1
CTC															1
CTG	2															1
GAA	5
GAC	12																					2
GAG	6											1										3
GAT	1																						1		1
GCA																						1
GCC	3																										1
GCG	13									1																1
GCT	1
GGA																														1
GGC	7					1
GGG	11																											1
GGT	1
GTA	7																																1
GTC	1								1																						1
GTG	2									2
GTT																																		1
TAA
TAC																																			1
TAG																																							1
TCA
TCC	1																	1																		1
TCG																																									1
TCT																																										1
TGC
TGT																																								2
TTA																																					1
TTC	1
TTG
TTT

	*	-	?	A	C	D	E	F	G	H	I	L	M	N	P	Q	R	S	T	V	Y
*																		1
-			1				2			1				1					1
?
A		17		2			1						1
C					2
D		13				2	2
E		11					3									1
F		1
G		19							2									1
H		1								4				1	1		2
I		1																		1
L		3									1	1			2			1
M
N		1																1
P		6		1					2			1					1	2
Q																1
R		3													1				1
S		7						1	1			1					1	1			1
T											1			2
V		10									1		2							3
Y	1

	-	AAC	AAT	ACA	ACT	AGC	AGT	ATA	ATC	ATG	CAC	CAG	CAT	CCA	CCC	CCG	CCT	CGC	CGG	CTC	CTG	GAA	GAC	GAG	GAT	GCC	GCT	GGA	GGC	GGT	GTA	GTC	GTG	GTT	TAA	TAC	TCA	TCC	TCG	TGC	TTG	TTT
-			1		1						1													2
AAC	1
AAT							1
ACA
ACC		2							1
ACT
AGA				1
AGC	6																												1
AGT						1
ATA	1
ATC																																1
ATG
CAA												1
CAC		1									1		3					2
CAG
CAT	1																1
CCA
CCC																										1												2
CCG	6																		1		1
CCT																														2
CGA														1
CGC
CGG	3
CTA	1							1												1
CTC															1
CTG	2															1
GAA	5
GAC	12																					2
GAG	6											1										3
GAT	1																						1		1
GCA																						1
GCC	3																										1
GCG	13									1																1
GCT	1
GGA																														1
GGC	7					1
GGG	11																											1
GGT	1
GTA	7																																1
GTC	1								1																						1
GTG	2									2
GTT																																		1
TAA
TAC																																			1
TAG																																							1
TCA
TCC	1																	1																		1
TCG																																									1
TCT																																										1
TGC
TGT																																								2
TTA																																					1
TTC	1
TTG
TTT

	*	-	?	A	C	D	E	F	G	H	I	L	M	N	P	Q	R	S	T	V	Y
*																		1
-			1				2			1				1					1
?
A		17		2			1						1
C					2
D		13				2	2
E		11					3									1
F		1
G		19							2									1
H		1								4				1	1		2
I		1																		1
L		3									1	1			2			1
M
N		1																1
P		6		1					2			1					1	2
Q																1
R		3													1				1
S		7						1	1			1					1	1			1
T											1			2
V		10									1		2							3
Y	1