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 2026-06-08 20:38

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

Command line arguments
SnpEff GRCh38.105 -csvStats HCC1395_BL_custom.ann_snpEff.csv HCC1395_BL_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) 2

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 16

Genome total length 63,147,197,748

Genome effective length 387,351,139

Variant rate 1 variant every 193,675,569 bases

Variants rate details

Chromosome Length Variants Variants rate

1 248,956,422 1 248,956,422

9 138,394,717 1 138,394,717

Total 387,351,139 2 193,675,569

Chromosome	Length	Variants	Variants rate
1	248,956,422	1	248,956,422
9	138,394,717	1	138,394,717
Total	387,351,139	2	193,675,569

Number variants by type

Type Total

SNP 0

MNP 0

INS 0

DEL 2

MIXED 0

INV 0

DUP 0

BND 0

INTERVAL 0

Total 2

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

Number of effects by impact

Type (alphabetical order) Count Percent

HIGH 10 62.5%

LOW 1 6.25%

MODIFIER 5 31.25%

Type (alphabetical order)	Count	Percent
HIGH	10	62.5%
LOW	1	6.25%
MODIFIER	5	31.25%

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 5.556%

conservative_inframe_deletion 1 5.556%

downstream_gene_variant 1 5.556%

exon_loss_variant 7 38.889%

gene_fusion 1 5.556%

intron_variant 3 16.667%

non_coding_transcript_exon_variant 1 5.556%

splice_region_variant 1 5.556%

start_lost 1 5.556%

upstream_gene_variant 1 5.556%

Type (alphabetical order) Count Percent

DOWNSTREAM 1 6.25%

EXON 8 50%

GENE 2 12.5%

INTRON 3 18.75%

SPLICE_SITE_REGION 1 6.25%

UPSTREAM 1 6.25%

Quality:

Insertions and deletions length:

	
		 Min 1  
		 Max 1  
		 Mean 1  
		 Median 1  
		 Standard deviation 0  
		 Values 1  
		 Count 2

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	50
Mean	50
Median	50
Standard deviation	0
Values	50
Count	2

Allele Count

Min	1
Max	1
Mean	1
Median	1
Standard deviation	0
Values	1
Count	2

Hom/Het per sample

Sample_names , 3574109522_sv1
Reference , 0
Het , 2
Hom , 0
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 ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCT CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCT GGA GGC GGG GGT GTA GTC GTG TAC TAG TAT TCA TCC TCT TGC TGG TGT TTC TTG TTT

-

AAA 2

AAC 6

AAG 18

AAT 4

ACA 2

ACC 2

ACG 1

ACT 1

AGA 2

AGC 6

ATA 2

ATC 9

ATG 9

ATT 4

CAA 1

CAC 4

CAG 5

CAT 1

CCA 6

CCC 4

CCT 3

CGC 5

CGG 1

CGT 2

CTA 1

CTC 6

CTG 16

CTT 1

GAA 7

GAC 10

GAG 11

GAT 4

GCA 1

GCC 8

GCT 3

GGA 1

GGC 4

GGG 8

GGT 1

GTA 1

GTC 3

GTG 3

TAC 9

TAG 1

TAT 3

TCA 3

TCC 3

TCT 1

TGC 3

TGG 4

TGT 1

TTC 7

TTG 6

TTT 8

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 12

C 4

D 14

E 18

F 15

G 14

H 5

I 15

K 20

L 30

M 9

N 10

P 13

Q 6

R 10

S 13

T 6

V 7

W 4

Y 12

Variants by chromosome

		

		1, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000,139000000,140000000,141000000,142000000,143000000,144000000,145000000,146000000,147000000,148000000,149000000,150000000,151000000,152000000,153000000,154000000,155000000,156000000,157000000,158000000,159000000,160000000,161000000,162000000,163000000,164000000,165000000,166000000,167000000,168000000,169000000,170000000,171000000,172000000,173000000,174000000,175000000,176000000,177000000,178000000,179000000,180000000,181000000,182000000,183000000,184000000,185000000,186000000,187000000,188000000,189000000,190000000,191000000,192000000,193000000,194000000,195000000,196000000,197000000,198000000,199000000,200000000,201000000,202000000,203000000,204000000,205000000,206000000,207000000,208000000,209000000,210000000,211000000,212000000,213000000,214000000,215000000,216000000,217000000,218000000,219000000,220000000,221000000,222000000,223000000,224000000,225000000,226000000,227000000,228000000,229000000,230000000,231000000,232000000,233000000,234000000,235000000,236000000,237000000,238000000,239000000,240000000,241000000,242000000,243000000,244000000,245000000,246000000,247000000,248000000
1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

		

		9, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000
9,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

Details by gene

Here you can find a tab-separated table.

Genome	GRCh38.105
Date	2026-06-08 20:38
SnpEff version	SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
Command line arguments	SnpEff GRCh38.105 -csvStats HCC1395_BL_custom.ann_snpEff.csv HCC1395_BL_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)	2
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	16
Genome total length	63,147,197,748
Genome effective length	387,351,139
Variant rate	1 variant every 193,675,569 bases

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGA	AGC	ATA	ATC	ATG	ATT	CAA	CAC	CAG	CAT	CCA	CCC	CCT	CGC	CGG	CGT	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	TAC	TAG	TAT	TCA	TCC	TCT	TGC	TGG	TGT	TTC	TTG	TTT
-
AAA	2
AAC	6
AAG	18
AAT	4
ACA	2
ACC	2
ACG	1
ACT	1
AGA	2
AGC	6
ATA	2
ATC	9
ATG	9
ATT	4
CAA	1
CAC	4
CAG	5
CAT	1
CCA	6
CCC	4
CCT	3
CGC	5
CGG	1
CGT	2
CTA	1
CTC	6
CTG	16
CTT	1
GAA	7
GAC	10
GAG	11
GAT	4
GCA	1
GCC	8
GCT	3
GGA	1
GGC	4
GGG	8
GGT	1
GTA	1
GTC	3
GTG	3
TAC	9
TAG	1
TAT	3
TCA	3
TCC	3
TCT	1
TGC	3
TGG	4
TGT	1
TTC	7
TTG	6
TTT	8

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGA	AGC	ATA	ATC	ATG	ATT	CAA	CAC	CAG	CAT	CCA	CCC	CCT	CGC	CGG	CGT	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	TAC	TAG	TAT	TCA	TCC	TCT	TGC	TGG	TGT	TTC	TTG	TTT
-
AAA	2
AAC	6
AAG	18
AAT	4
ACA	2
ACC	2
ACG	1
ACT	1
AGA	2
AGC	6
ATA	2
ATC	9
ATG	9
ATT	4
CAA	1
CAC	4
CAG	5
CAT	1
CCA	6
CCC	4
CCT	3
CGC	5
CGG	1
CGT	2
CTA	1
CTC	6
CTG	16
CTT	1
GAA	7
GAC	10
GAG	11
GAT	4
GCA	1
GCC	8
GCT	3
GGA	1
GGC	4
GGG	8
GGT	1
GTA	1
GTC	3
GTG	3
TAC	9
TAG	1
TAT	3
TCA	3
TCC	3
TCT	1
TGC	3
TGG	4
TGT	1
TTC	7
TTG	6
TTT	8

	-	AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGA	AGC	ATA	ATC	ATG	ATT	CAA	CAC	CAG	CAT	CCA	CCC	CCT	CGC	CGG	CGT	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	TAC	TAG	TAT	TCA	TCC	TCT	TGC	TGG	TGT	TTC	TTG	TTT
-
AAA	2
AAC	6
AAG	18
AAT	4
ACA	2
ACC	2
ACG	1
ACT	1
AGA	2
AGC	6
ATA	2
ATC	9
ATG	9
ATT	4
CAA	1
CAC	4
CAG	5
CAT	1
CCA	6
CCC	4
CCT	3
CGC	5
CGG	1
CGT	2
CTA	1
CTC	6
CTG	16
CTT	1
GAA	7
GAC	10
GAG	11
GAT	4
GCA	1
GCC	8
GCT	3
GGA	1
GGC	4
GGG	8
GGT	1
GTA	1
GTC	3
GTG	3
TAC	9
TAG	1
TAT	3
TCA	3
TCC	3
TCT	1
TGC	3
TGG	4
TGT	1
TTC	7
TTG	6
TTT	8