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 brucella_suis_cita_364

Date 2025-02-19 16:50

SnpEff version
SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani

Command line arguments
SnpEff -csvStats CRG4_struct.snpEff_summary.csv -htmlStats CRG4_struct.snpEff_summary.html brucella_suis_cita_364 CRG4_struct.vcf

Warnings 51

Errors 2

Number of lines (input file) 20

Number of variants (before filter) 17

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

Number of variants processed
(i.e. after filter and non-variants) 17

Number of known variants
(i.e. non-empty ID) 17 ( 100% )

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

Number of effects 374

Genome total length 3,328,972

Genome effective length 3,328,972

Variant rate 1 variant every 195,821 bases

Variants rate details

Chromosome Length Variants Variants rate

NZ_CP007697.1 1,927,594 12 160,632

NZ_CP007698.1 1,401,378 5 280,275

Total 3,328,972 17 195,821

Chromosome	Length	Variants	Variants rate
NZ_CP007697.1	1,927,594	12	160,632
NZ_CP007698.1	1,401,378	5	280,275
Total	3,328,972	17	195,821

Number variants by type

Type Total

SNP 0

MNP 0

INS 0

DEL 15

MIXED 0

INV 0

DUP 2

BND 0

INTERVAL 0

Total 17

Type	Total
SNP	0
MNP	0
INS	0
DEL	15
MIXED	0
INV	0
DUP	2
BND	0
INTERVAL	0
Total	17

Number of effects by impact

Type (alphabetical order) Count Percent

HIGH 192 51.337%

MODERATE 5 1.337%

MODIFIER 177 47.326%

Type (alphabetical order)	Count	Percent
HIGH	192	51.337%
MODERATE	5	1.337%
MODIFIER	177	47.326%

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 5 1.279%

chromosome_number_variation 2 0.512%

conservative_inframe_deletion 6 1.535%

downstream_gene_variant 71 18.159%

duplication 3 0.767%

exon_loss_variant 4 1.023%

feature_ablation 47 12.02%

frameshift_variant 8 2.046%

gene_fusion 5 1.279%

intragenic_variant 7 1.79%

intron_variant 16 4.092%

splice_region_variant 5 1.279%

start_lost 7 1.79%

stop_lost 5 1.279%

transcript_ablation 117 29.923%

upstream_gene_variant 83 21.228%

Type (alphabetical order) Count Percent

CHROMOSOME 2 0.535%

DOWNSTREAM 71 18.984%

EXON 18 4.813%

GENE 59 15.775%

INTRON 16 4.278%

TRANSCRIPT 125 33.422%

UPSTREAM 83 22.193%

Quality:

Insertions and deletions length:

	
		 Min 1  
		 Max 1  
		 Mean 1  
		 Median 1  
		 Standard deviation 0  
		 Values 1  
		 Count 15

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

Allele Count

Min	1
Max	1
Mean	1
Median	1
Standard deviation	0
Values	1
Count	20

Hom/Het per sample

Sample_names 
Reference 
Het 
Hom 
Missing

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 CGT CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT

-

AAA 21

AAC 14

AAG 74

AAT 30

ACA 7

ACC 29

ACG 21

ACT 4

AGA 8

AGC 19

AGG 11

AGT 3

ATA 8

ATC 54

ATG 36

ATT 39

CAA 14

CAC 22

CAG 37

CAT 17

CCA 10

CCC 16

CCG 41

CCT 10

CGA 8

CGC 54

CGG 17

CGT 25

CTA 8

CTC 18

CTG 62

CTT 49

GAA 75

GAC 65

GAG 57

GAT 56

GCA 35

GCC 75

GCG 79

GCT 48

GGA 14

GGC 88

GGG 18

GGT 15

GTA 5

GTC 27

GTG 36

GTT 32

TAA 2

TAC 20

TAG 1

TAT 29

TCA 8

TCC 16

TCG 27

TCT 4

TGA 2

TGC 13

TGG 24

TGT 4

TTA 2

TTC 54

TTG 22

TTT 25

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

* 5

-

A 237

C 17

D 121

E 132

F 79

G 135

H 39

I 101

K 95

L 161

M 36

N 44

P 77

Q 51

R 123

S 77

T 61

V 100

W 24

Y 49

Variants by chromosome

		

		NZ_CP007697.1, Position,0,10000,20000,30000,40000,50000,60000,70000,80000,90000,100000,110000,120000,130000,140000,150000,160000,170000,180000,190000,200000,210000,220000,230000,240000,250000,260000,270000,280000,290000,300000,310000,320000,330000,340000,350000,360000,370000,380000,390000,400000,410000,420000,430000,440000,450000,460000,470000,480000,490000,500000,510000,520000,530000,540000,550000,560000,570000,580000,590000,600000,610000,620000,630000,640000,650000,660000,670000,680000,690000,700000,710000,720000,730000,740000,750000,760000,770000,780000,790000,800000,810000,820000,830000,840000,850000,860000,870000,880000,890000,900000,910000,920000,930000,940000,950000,960000,970000,980000,990000,1000000,1010000,1020000,1030000,1040000,1050000,1060000,1070000,1080000,1090000,1100000,1110000,1120000,1130000,1140000,1150000,1160000,1170000,1180000,1190000,1200000,1210000,1220000,1230000,1240000,1250000,1260000,1270000,1280000,1290000,1300000,1310000,1320000,1330000,1340000,1350000,1360000,1370000,1380000,1390000,1400000,1410000,1420000,1430000,1440000,1450000,1460000,1470000,1480000,1490000,1500000,1510000,1520000,1530000,1540000,1550000,1560000,1570000,1580000,1590000,1600000,1610000,1620000,1630000,1640000,1650000,1660000,1670000,1680000,1690000,1700000,1710000,1720000,1730000,1740000,1750000,1760000,1770000,1780000,1790000,1800000,1810000,1820000,1830000,1840000,1850000,1860000,1870000,1880000,1890000,1900000,1910000,1920000
NZ_CP007697.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0

		

		NZ_CP007698.1, Position,0,10000,20000,30000,40000,50000,60000,70000,80000,90000,100000,110000,120000,130000,140000,150000,160000,170000,180000,190000,200000,210000,220000,230000,240000,250000,260000,270000,280000,290000,300000,310000,320000,330000,340000,350000,360000,370000,380000,390000,400000,410000,420000,430000,440000,450000,460000,470000,480000,490000,500000,510000,520000,530000,540000,550000,560000,570000,580000,590000,600000,610000,620000,630000,640000,650000,660000,670000,680000,690000,700000,710000,720000,730000,740000,750000,760000,770000,780000,790000,800000,810000,820000,830000,840000,850000,860000,870000,880000,890000,900000,910000,920000,930000,940000,950000,960000,970000,980000,990000,1000000,1010000,1020000,1030000,1040000,1050000,1060000,1070000,1080000,1090000,1100000,1110000,1120000,1130000,1140000,1150000,1160000,1170000,1180000,1190000,1200000,1210000,1220000,1230000,1240000,1250000,1260000,1270000,1280000,1290000,1300000,1310000,1320000,1330000,1340000,1350000,1360000,1370000,1380000,1390000,1400000
NZ_CP007698.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

Details by gene

Here you can find a tab-separated table.

Genome	brucella_suis_cita_364
Date	2025-02-19 16:50
SnpEff version	SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Command line arguments	SnpEff -csvStats CRG4_struct.snpEff_summary.csv -htmlStats CRG4_struct.snpEff_summary.html brucella_suis_cita_364 CRG4_struct.vcf
Warnings	51
Errors	2
Number of lines (input file)	20
Number of variants (before filter)	17
Number of not variants (i.e. reference equals alternative)	0
Number of variants processed (i.e. after filter and non-variants)	17
Number of known variants (i.e. non-empty ID)	17 ( 100% )
Number of multi-allelic VCF entries (i.e. more than two alleles)	0
Number of effects	374
Genome total length	3,328,972
Genome effective length	3,328,972
Variant rate	1 variant every 195,821 bases

	-	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	CGT	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCG	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	GTT	TAA	TAC	TAG	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	21
AAC	14
AAG	74
AAT	30
ACA	7
ACC	29
ACG	21
ACT	4
AGA	8
AGC	19
AGG	11
AGT	3
ATA	8
ATC	54
ATG	36
ATT	39
CAA	14
CAC	22
CAG	37
CAT	17
CCA	10
CCC	16
CCG	41
CCT	10
CGA	8
CGC	54
CGG	17
CGT	25
CTA	8
CTC	18
CTG	62
CTT	49
GAA	75
GAC	65
GAG	57
GAT	56
GCA	35
GCC	75
GCG	79
GCT	48
GGA	14
GGC	88
GGG	18
GGT	15
GTA	5
GTC	27
GTG	36
GTT	32
TAA	2
TAC	20
TAG	1
TAT	29
TCA	8
TCC	16
TCG	27
TCT	4
TGA	2
TGC	13
TGG	24
TGT	4
TTA	2
TTC	54
TTG	22
TTT	25

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		5
-
A		237
C		17
D		121
E		132
F		79
G		135
H		39
I		101
K		95
L		161
M		36
N		44
P		77
Q		51
R		123
S		77
T		61
V		100
W		24
Y		49

	-	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	CGT	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCG	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	GTT	TAA	TAC	TAG	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	21
AAC	14
AAG	74
AAT	30
ACA	7
ACC	29
ACG	21
ACT	4
AGA	8
AGC	19
AGG	11
AGT	3
ATA	8
ATC	54
ATG	36
ATT	39
CAA	14
CAC	22
CAG	37
CAT	17
CCA	10
CCC	16
CCG	41
CCT	10
CGA	8
CGC	54
CGG	17
CGT	25
CTA	8
CTC	18
CTG	62
CTT	49
GAA	75
GAC	65
GAG	57
GAT	56
GCA	35
GCC	75
GCG	79
GCT	48
GGA	14
GGC	88
GGG	18
GGT	15
GTA	5
GTC	27
GTG	36
GTT	32
TAA	2
TAC	20
TAG	1
TAT	29
TCA	8
TCC	16
TCG	27
TCT	4
TGA	2
TGC	13
TGG	24
TGT	4
TTA	2
TTC	54
TTG	22
TTT	25

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		5
-
A		237
C		17
D		121
E		132
F		79
G		135
H		39
I		101
K		95
L		161
M		36
N		44
P		77
Q		51
R		123
S		77
T		61
V		100
W		24
Y		49

	-	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	CGT	CTA	CTC	CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCG	GCT	GGA	GGC	GGG	GGT	GTA	GTC	GTG	GTT	TAA	TAC	TAG	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	21
AAC	14
AAG	74
AAT	30
ACA	7
ACC	29
ACG	21
ACT	4
AGA	8
AGC	19
AGG	11
AGT	3
ATA	8
ATC	54
ATG	36
ATT	39
CAA	14
CAC	22
CAG	37
CAT	17
CCA	10
CCC	16
CCG	41
CCT	10
CGA	8
CGC	54
CGG	17
CGT	25
CTA	8
CTC	18
CTG	62
CTT	49
GAA	75
GAC	65
GAG	57
GAT	56
GCA	35
GCC	75
GCG	79
GCT	48
GGA	14
GGC	88
GGG	18
GGT	15
GTA	5
GTC	27
GTG	36
GTT	32
TAA	2
TAC	20
TAG	1
TAT	29
TCA	8
TCC	16
TCG	27
TCT	4
TGA	2
TGC	13
TGG	24
TGT	4
TTA	2
TTC	54
TTG	22
TTT	25

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		5
-
A		237
C		17
D		121
E		132
F		79
G		135
H		39
I		101
K		95
L		161
M		36
N		44
P		77
Q		51
R		123
S		77
T		61
V		100
W		24
Y		49