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 CRG5_fix_struct.snpEff_summary.csv -htmlStats CRG5_fix_struct.snpEff_summary.html brucella_suis_cita_364_fix CRG5_fix_struct.vcf

Warnings 31

Errors 3

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 430

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 273 63.488%

LOW 1 0.233%

MODERATE 5 1.163%

MODIFIER 151 35.116%

Type (alphabetical order)	Count	Percent
HIGH	273	63.488%
LOW	1	0.233%
MODERATE	5	1.163%
MODIFIER	151	35.116%

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 2 0.44%

chromosome_number_variation 3 0.659%

conservative_inframe_deletion 5 1.099%

downstream_gene_variant 67 14.725%

duplication 4 0.879%

exon_loss_variant 6 1.319%

feature_ablation 67 14.725%

frameshift_variant 16 3.516%

gene_fusion 1 0.22%

intergenic_region 11 2.418%

splice_region_variant 9 1.978%

start_lost 7 1.538%

stop_lost 9 1.978%

transcript_ablation 175 38.462%

upstream_gene_variant 73 16.044%

Type (alphabetical order) Count Percent

CHROMOSOME 3 0.698%

DOWNSTREAM 67 15.581%

EXON 28 6.512%

GENE 71 16.512%

INTERGENIC 11 2.558%

TRANSCRIPT 177 41.163%

UPSTREAM 73 16.977%

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 22

AAC 20

AAG 78

AAT 34

ACA 7

ACC 36

ACG 27

ACT 4

AGA 8

AGC 19

AGG 10

AGT 3

ATA 8

ATC 70

ATG 46

ATT 45

CAA 14

CAC 25

CAG 41

CAT 16

CCA 12

CCC 19

CCG 46

CCT 10

CGA 8

CGC 61

CGG 21

CGT 27

CTA 8

CTC 23

CTG 68

CTT 49

GAA 80

GAC 70

GAG 63

GAT 65

GCA 44

GCC 82

GCG 86

GCT 54

GGA 14

GGC 103

GGG 19

GGT 17

GTA 4

GTC 33

GTG 36

GTT 34

TAA 2

TAC 21

TAT 29

TCA 9

TCC 18

TCG 31

TCT 4

TGA 7

TGC 17

TGG 27

TGT 4

TTA 2

TTC 56

TTG 25

TTT 27

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 266

C 21

D 135

E 143

F 83

G 153

H 41

I 123

K 100

L 175

M 46

N 54

P 87

Q 55

R 135

S 84

T 74

V 107

W 27

Y 50

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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0

		

		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 CRG5_fix_struct.snpEff_summary.csv -htmlStats CRG5_fix_struct.snpEff_summary.html brucella_suis_cita_364_fix CRG5_fix_struct.vcf
Warnings	31
Errors	3
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	430
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	22
AAC	20
AAG	78
AAT	34
ACA	7
ACC	36
ACG	27
ACT	4
AGA	8
AGC	19
AGG	10
AGT	3
ATA	8
ATC	70
ATG	46
ATT	45
CAA	14
CAC	25
CAG	41
CAT	16
CCA	12
CCC	19
CCG	46
CCT	10
CGA	8
CGC	61
CGG	21
CGT	27
CTA	8
CTC	23
CTG	68
CTT	49
GAA	80
GAC	70
GAG	63
GAT	65
GCA	44
GCC	82
GCG	86
GCT	54
GGA	14
GGC	103
GGG	19
GGT	17
GTA	4
GTC	33
GTG	36
GTT	34
TAA	2
TAC	21
TAT	29
TCA	9
TCC	18
TCG	31
TCT	4
TGA	7
TGC	17
TGG	27
TGT	4
TTA	2
TTC	56
TTG	25
TTT	27

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		9
-
A		266
C		21
D		135
E		143
F		83
G		153
H		41
I		123
K		100
L		175
M		46
N		54
P		87
Q		55
R		135
S		84
T		74
V		107
W		27
Y		50

	-	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	22
AAC	20
AAG	78
AAT	34
ACA	7
ACC	36
ACG	27
ACT	4
AGA	8
AGC	19
AGG	10
AGT	3
ATA	8
ATC	70
ATG	46
ATT	45
CAA	14
CAC	25
CAG	41
CAT	16
CCA	12
CCC	19
CCG	46
CCT	10
CGA	8
CGC	61
CGG	21
CGT	27
CTA	8
CTC	23
CTG	68
CTT	49
GAA	80
GAC	70
GAG	63
GAT	65
GCA	44
GCC	82
GCG	86
GCT	54
GGA	14
GGC	103
GGG	19
GGT	17
GTA	4
GTC	33
GTG	36
GTT	34
TAA	2
TAC	21
TAT	29
TCA	9
TCC	18
TCG	31
TCT	4
TGA	7
TGC	17
TGG	27
TGT	4
TTA	2
TTC	56
TTG	25
TTT	27

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		9
-
A		266
C		21
D		135
E		143
F		83
G		153
H		41
I		123
K		100
L		175
M		46
N		54
P		87
Q		55
R		135
S		84
T		74
V		107
W		27
Y		50

	-	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	22
AAC	20
AAG	78
AAT	34
ACA	7
ACC	36
ACG	27
ACT	4
AGA	8
AGC	19
AGG	10
AGT	3
ATA	8
ATC	70
ATG	46
ATT	45
CAA	14
CAC	25
CAG	41
CAT	16
CCA	12
CCC	19
CCG	46
CCT	10
CGA	8
CGC	61
CGG	21
CGT	27
CTA	8
CTC	23
CTG	68
CTT	49
GAA	80
GAC	70
GAG	63
GAT	65
GCA	44
GCC	82
GCG	86
GCT	54
GGA	14
GGC	103
GGG	19
GGT	17
GTA	4
GTC	33
GTG	36
GTT	34
TAA	2
TAC	21
TAT	29
TCA	9
TCC	18
TCG	31
TCT	4
TGA	7
TGC	17
TGG	27
TGT	4
TTA	2
TTC	56
TTG	25
TTT	27

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		9
-
A		266
C		21
D		135
E		143
F		83
G		153
H		41
I		123
K		100
L		175
M		46
N		54
P		87
Q		55
R		135
S		84
T		74
V		107
W		27
Y		50