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_fix

Date 2025-02-24 16:30

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

Command line arguments
SnpEff -csvStats CRG6_fix_struct.snpEff_summary.csv -htmlStats CRG6_fix_struct.snpEff_summary.html brucella_suis_cita_364_fix CRG6_fix_struct.vcf

Warnings 37

Errors 4

Number of lines (input file) 19

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 507

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

OOAJICEE_1 1,927,594 13 148,276

OOAJICEE_2 1,401,378 4 350,344

Total 3,328,972 17 195,821

Chromosome	Length	Variants	Variants rate
OOAJICEE_1	1,927,594	13	148,276
OOAJICEE_2	1,401,378	4	350,344
Total	3,328,972	17	195,821

Number variants by type

Type Total

SNP 0

MNP 0

INS 0

DEL 16

MIXED 0

INV 0

DUP 1

BND 0

INTERVAL 0

Total 17

Type	Total
SNP	0
MNP	0
INS	0
DEL	16
MIXED	0
INV	0
DUP	1
BND	0
INTERVAL	0
Total	17

Number of effects by impact

Type (alphabetical order) Count Percent

HIGH 357 70.414%

LOW 1 0.197%

MODERATE 5 0.986%

MODIFIER 144 28.402%

Type (alphabetical order)	Count	Percent
HIGH	357	70.414%
LOW	1	0.197%
MODERATE	5	0.986%
MODIFIER	144	28.402%

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 3 0.56%

chromosome_number_variation 4 0.746%

conservative_inframe_deletion 5 0.933%

downstream_gene_variant 60 11.194%

duplication 4 0.746%

exon_loss_variant 8 1.493%

feature_ablation 90 16.791%

frameshift_variant 19 3.545%

gene_fusion 1 0.187%

intergenic_region 11 2.052%

intragenic_variant 2 0.373%

splice_region_variant 9 1.679%

start_lost 11 2.052%

stop_lost 9 1.679%

transcript_ablation 229 42.724%

upstream_gene_variant 71 13.246%

Type (alphabetical order) Count Percent

CHROMOSOME 4 0.789%

DOWNSTREAM 60 11.834%

EXON 33 6.509%

GENE 95 18.738%

INTERGENIC 11 2.17%

TRANSCRIPT 233 45.957%

UPSTREAM 71 14.004%

Quality:

Insertions and deletions length:

	
		 Min 1  
		 Max 1  
		 Mean 1  
		 Median 1  
		 Standard deviation 0  
		 Values 1  
		 Count 16

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	19

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 TAT TCA TCC TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT

-

AAA 28

AAC 28

AAG 108

AAT 54

ACA 11

ACC 66

ACG 47

ACT 6

AGA 10

AGC 29

AGG 12

AGT 5

ATA 8

ATC 100

ATG 60

ATT 61

CAA 20

CAC 27

CAG 71

CAT 22

CCA 14

CCC 35

CCG 60

CCT 14

CGA 8

CGC 98

CGG 29

CGT 35

CTA 10

CTC 41

CTG 94

CTT 67

GAA 110

GAC 90

GAG 79

GAT 97

GCA 68

GCC 138

GCG 122

GCT 64

GGA 18

GGC 139

GGG 21

GGT 25

GTA 6

GTC 61

GTG 68

GTT 46

TAA 2

TAC 25

TAT 43

TCA 11

TCC 34

TCG 39

TCT 10

TGA 7

TGC 19

TGG 35

TGT 4

TTA 2

TTC 64

TTG 31

TTT 31

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

* 9

-

A 392

C 23

D 187

E 189

F 95

G 203

H 49

I 169

K 136

L 245

M 60

N 82

P 123

Q 91

R 192

S 128

T 130

V 181

W 35

Y 68

Variants by chromosome

		

		OOAJICEE_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
OOAJICEE_1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0

		

		OOAJICEE_2, 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
OOAJICEE_2,Count,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0

Details by gene

Here you can find a tab-separated table.

Genome	brucella_suis_cita_364_fix
Date	2025-02-24 16:30
SnpEff version	SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Command line arguments	SnpEff -csvStats CRG6_fix_struct.snpEff_summary.csv -htmlStats CRG6_fix_struct.snpEff_summary.html brucella_suis_cita_364_fix CRG6_fix_struct.vcf
Warnings	37
Errors	4
Number of lines (input file)	19
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	507
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	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	28
AAC	28
AAG	108
AAT	54
ACA	11
ACC	66
ACG	47
ACT	6
AGA	10
AGC	29
AGG	12
AGT	5
ATA	8
ATC	100
ATG	60
ATT	61
CAA	20
CAC	27
CAG	71
CAT	22
CCA	14
CCC	35
CCG	60
CCT	14
CGA	8
CGC	98
CGG	29
CGT	35
CTA	10
CTC	41
CTG	94
CTT	67
GAA	110
GAC	90
GAG	79
GAT	97
GCA	68
GCC	138
GCG	122
GCT	64
GGA	18
GGC	139
GGG	21
GGT	25
GTA	6
GTC	61
GTG	68
GTT	46
TAA	2
TAC	25
TAT	43
TCA	11
TCC	34
TCG	39
TCT	10
TGA	7
TGC	19
TGG	35
TGT	4
TTA	2
TTC	64
TTG	31
TTT	31

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		9
-
A		392
C		23
D		187
E		189
F		95
G		203
H		49
I		169
K		136
L		245
M		60
N		82
P		123
Q		91
R		192
S		128
T		130
V		181
W		35
Y		68

	-	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	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	28
AAC	28
AAG	108
AAT	54
ACA	11
ACC	66
ACG	47
ACT	6
AGA	10
AGC	29
AGG	12
AGT	5
ATA	8
ATC	100
ATG	60
ATT	61
CAA	20
CAC	27
CAG	71
CAT	22
CCA	14
CCC	35
CCG	60
CCT	14
CGA	8
CGC	98
CGG	29
CGT	35
CTA	10
CTC	41
CTG	94
CTT	67
GAA	110
GAC	90
GAG	79
GAT	97
GCA	68
GCC	138
GCG	122
GCT	64
GGA	18
GGC	139
GGG	21
GGT	25
GTA	6
GTC	61
GTG	68
GTT	46
TAA	2
TAC	25
TAT	43
TCA	11
TCC	34
TCG	39
TCT	10
TGA	7
TGC	19
TGG	35
TGT	4
TTA	2
TTC	64
TTG	31
TTT	31

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		9
-
A		392
C		23
D		187
E		189
F		95
G		203
H		49
I		169
K		136
L		245
M		60
N		82
P		123
Q		91
R		192
S		128
T		130
V		181
W		35
Y		68

	-	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	TAT	TCA	TCC	TCG	TCT	TGA	TGC	TGG	TGT	TTA	TTC	TTG	TTT
-
AAA	28
AAC	28
AAG	108
AAT	54
ACA	11
ACC	66
ACG	47
ACT	6
AGA	10
AGC	29
AGG	12
AGT	5
ATA	8
ATC	100
ATG	60
ATT	61
CAA	20
CAC	27
CAG	71
CAT	22
CCA	14
CCC	35
CCG	60
CCT	14
CGA	8
CGC	98
CGG	29
CGT	35
CTA	10
CTC	41
CTG	94
CTT	67
GAA	110
GAC	90
GAG	79
GAT	97
GCA	68
GCC	138
GCG	122
GCT	64
GGA	18
GGC	139
GGG	21
GGT	25
GTA	6
GTC	61
GTG	68
GTT	46
TAA	2
TAC	25
TAT	43
TCA	11
TCC	34
TCG	39
TCT	10
TGA	7
TGC	19
TGG	35
TGT	4
TTA	2
TTC	64
TTG	31
TTT	31

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		9
-
A		392
C		23
D		187
E		189
F		95
G		203
H		49
I		169
K		136
L		245
M		60
N		82
P		123
Q		91
R		192
S		128
T		130
V		181
W		35
Y		68