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 21:42

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.mutect2.whatshap.phased_custom.ann_snpEff.csv HCC1395_tumor_vs_HCC1395_BL.mutect2.whatshap.phased_custom.ann.vcf.gz

Warnings 3

Errors 0

Number of lines (input file) 44

Number of variants (before filter) 68

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

Number of variants processed
(i.e. after filter and non-variants) 68

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

Number of multi-allelic VCF entries
(i.e. more than two alleles) 9

Number of effects 94

Genome total length 63,147,197,748

Genome effective length 46,709,983

Variant rate 1 variant every 686,911 bases

Variants rate details

Chromosome Length Variants Variants rate

21 46,709,983 68 686,911

Total 46,709,983 68 686,911

Chromosome	Length	Variants	Variants rate
21	46,709,983	68	686,911
Total	46,709,983	68	686,911

Number variants by type

Type Total

SNP 28

MNP 3

INS 12

DEL 25

MIXED 0

INV 0

DUP 0

BND 0

INTERVAL 0

Total 68

Type	Total
SNP	28
MNP	3
INS	12
DEL	25
MIXED	0
INV	0
DUP	0
BND	0
INTERVAL	0
Total	68

Number of effects by impact

Type (alphabetical order) Count Percent

HIGH 1 1.064%

LOW 9 9.574%

MODERATE 21 22.34%

MODIFIER 63 67.021%

Type (alphabetical order)	Count	Percent
HIGH	1	1.064%
LOW	9	9.574%
MODERATE	21	22.34%
MODIFIER	63	67.021%

Number of effects by functional class

Type (alphabetical order) Count Percent

MISSENSE 11 55%

NONSENSE 1 5%

SILENT 8 40%

Type (alphabetical order)	Count	Percent
MISSENSE	11	55%
NONSENSE	1	5%
SILENT	8	40%

Missense / Silent ratio: 1.375

Number of effects by type and region

Type Region

Type (alphabetical order) Count Percent

3_prime_UTR_variant 5 5.208%

5_prime_UTR_variant 5 5.208%

conservative_inframe_deletion 4 4.167%

conservative_inframe_insertion 1 1.042%

disruptive_inframe_deletion 3 3.125%

downstream_gene_variant 12 12.5%

intragenic_variant 3 3.125%

intron_variant 30 31.25%

missense_variant 13 13.542%

non_coding_transcript_exon_variant 6 6.25%

splice_region_variant 2 2.083%

stop_gained 1 1.042%

synonymous_variant 8 8.333%

upstream_gene_variant 3 3.125%

Type (alphabetical order) Count Percent

DOWNSTREAM 12 12.766%

EXON 34 36.17%

INTRON 30 31.915%

SPLICE_SITE_REGION 2 2.128%

TRANSCRIPT 3 3.191%

UPSTREAM 3 3.191%

UTR_3_PRIME 5 5.319%

UTR_5_PRIME 5 5.319%

Quality:

Insertions and deletions length:

	
		 Min 0  
		 Max 3  
		 Mean 0.973  
		 Median 1  
		 Standard deviation 0.499  
		 Values 0,1,2,3  
		 Count 4,31,1,1

Min	0
Max	3
Mean	0.973
Median	1
Standard deviation	0.499
Values	0,1,2,3
Count	4,31,1,1

Base changes (SNPs)

A C G T

A 0 2 2 1

C 3 0 0 8

G 4 2 0 4

T 0 2 0 0

	A	C	G	T
A	0	2	2	1
C	3	0	0	8
G	4	2	0	4
T	0	2	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	16
Transversions	11
Ts/Tv ratio	1.4545

All variants:

Sample ,HCC1395_HCC1395_BL,HCC1395_HCC1395_tumor,Total
Transitions ,0,16,16
Transversions ,0,11,11
Ts/Tv ,NaN,1.455,1.455

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

No results available (empty input?)

Allele frequency

Min	25
Max	150
Mean	38.636
Median	25
Standard deviation	33.434
Values	25,50,75,125,150
Count	35,4,1,2,2

Allele Count

Min	1
Max	6
Mean	1.545
Median	1
Standard deviation	1.337
Values	1,2,3,5,6
Count	35,4,1,2,2

Hom/Het per sample

Sample_names , HCC1395_HCC1395_BL, HCC1395_HCC1395_tumor
Reference , 44, 0
Het , 0, 35
Hom , 0, 4
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 ACA ACC ACG AGA AGC AGG AGT ATC CAC CAG CAT CCC CCG CCT CGG CTA CTC CTG GAA GAC GAG GCA GCC GCG GCT GGC GGG GGT GTA GTC GTG TAA TAC TCA TCC TCG TCT TGC TGT

- 1

AAC 1

ACA 1

ACC 2 1 1

ACG 1

AGA 1

AGC 11

AGG 1

AGT 1

ATC 1

CAC 1 1 1

CAG 7

CAT 1 1

CCC 4 1 1

CCG 1

CCT 2

CGG 1

CTA 1

CTC 1

CTG 1

GAA

GAC 2

GAG 2 1

GCA 1

GCC 2

GCG 2 1

GCT 1

GGC 1

GGG 4

GGT

GTA

GTC 1

GTG 1 1

TAA

TAC 1

TCA

TCC 1 1 1

TCG 1

TCT

TGC

TGT 2

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 G H I L N P Q R S T V Y

*

- 1

A 5 1 1

C 2

D 2

E 2 1

G 4 1

H 1 2 1 1

I 1

L 3

N 1

P 5 1 2 1

Q 7

R 3

S 13 2 1

T 3 1 2

V 1 1 1

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,0,0,0,0,0,0,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,3,0,2,7,5,1,1,1,1,0,19,1,0,11,3,3

Details by gene

Here you can find a tab-separated table.

Genome	GRCh38.105
Date	2026-02-02 21:42
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.mutect2.whatshap.phased_custom.ann_snpEff.csv HCC1395_tumor_vs_HCC1395_BL.mutect2.whatshap.phased_custom.ann.vcf.gz
Warnings	3
Errors	0
Number of lines (input file)	44
Number of variants (before filter)	68
Number of not variants (i.e. reference equals alternative)	0
Number of variants processed (i.e. after filter and non-variants)	68
Number of known variants (i.e. non-empty ID)	0 ( 0% )
Number of multi-allelic VCF entries (i.e. more than two alleles)	9
Number of effects	94
Genome total length	63,147,197,748
Genome effective length	46,709,983
Variant rate	1 variant every 686,911 bases

	-	AAC	ACA	ACC	AGC	CAC	CAT	CCT	GAA	GAG	GCA	GCC	GGT	GTA	TAA	TAC	TCA	TCC	TCT	TGC
-						1
AAC	1
ACA	1
ACC	2	1	1
ACG			1
AGA	1
AGC	11
AGG	1
AGT	1
ATC				1
CAC		1				1	1
CAG	7
CAT	1							1
CCC	4											1						1
CCG	1
CCT													2
CGG	1
CTA	1
CTC	1
CTG	1
GAA
GAC									2
GAG	2								1
GCA									1
GCC	2
GCG	2										1
GCT	1
GGC					1
GGG	4
GGT
GTA
GTC														1
GTG	1									1
TAA
TAC															1
TCA
TCC	1															1			1
TCG																	1
TCT
TGC
TGT																				2

	-	AAC	ACA	ACC	AGC	CAC	CAT	CCT	GAA	GAG	GCA	GCC	GGT	GTA	TAA	TAC	TCA	TCC	TCT	TGC
-						1
AAC	1
ACA	1
ACC	2	1	1
ACG			1
AGA	1
AGC	11
AGG	1
AGT	1
ATC				1
CAC		1				1	1
CAG	7
CAT	1							1
CCC	4											1						1
CCG	1
CCT													2
CGG	1
CTA	1
CTC	1
CTG	1
GAA
GAC									2
GAG	2								1
GCA									1
GCC	2
GCG	2										1
GCT	1
GGC					1
GGG	4
GGT
GTA
GTC														1
GTG	1									1
TAA
TAC															1
TCA
TCC	1															1			1
TCG																	1
TCT
TGC
TGT																				2

	-	AAC	ACA	ACC	AGC	CAC	CAT	CCT	GAA	GAG	GCA	GCC	GGT	GTA	TAA	TAC	TCA	TCC	TCT	TGC
-						1
AAC	1
ACA	1
ACC	2	1	1
ACG			1
AGA	1
AGC	11
AGG	1
AGT	1
ATC				1
CAC		1				1	1
CAG	7
CAT	1							1
CCC	4											1						1
CCG	1
CCT													2
CGG	1
CTA	1
CTC	1
CTG	1
GAA
GAC									2
GAG	2								1
GCA									1
GCC	2
GCG	2										1
GCT	1
GGC					1
GGG	4
GGT
GTA
GTC														1
GTG	1									1
TAA
TAC															1
TCA
TCC	1															1			1
TCG																	1
TCT
TGC
TGT																				2