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 CRG1_fix_struct.snpEff_summary.csv -htmlStats CRG1_fix_struct.snpEff_summary.html brucella_suis_cita_364_fix CRG1_fix_struct.vcf

Warnings 32

Errors 3

Number of lines (input file) 22

Number of variants (before filter) 20

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

Number of variants processed
(i.e. after filter and non-variants) 20

Number of known variants
(i.e. non-empty ID) 20 ( 100% )

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

Number of effects 467

Genome total length 3,328,972

Genome effective length 3,328,972

Variant rate 1 variant every 166,448 bases

Variants rate details

Chromosome Length Variants Variants rate

OOAJICEE_1 1,927,594 16 120,474

OOAJICEE_2 1,401,378 4 350,344

Total 3,328,972 20 166,448

Chromosome	Length	Variants	Variants rate
OOAJICEE_1	1,927,594	16	120,474
OOAJICEE_2	1,401,378	4	350,344
Total	3,328,972	20	166,448

Number variants by type

Type Total

SNP 0

MNP 0

INS 0

DEL 19

MIXED 0

INV 0

DUP 1

BND 0

INTERVAL 0

Total 20

Type	Total
SNP	0
MNP	0
INS	0
DEL	19
MIXED	0
INV	0
DUP	1
BND	0
INTERVAL	0
Total	20

Number of effects by impact

Type (alphabetical order) Count Percent

HIGH 275 58.887%

LOW 1 0.214%

MODERATE 6 1.285%

MODIFIER 185 39.615%

Type (alphabetical order)	Count	Percent
HIGH	275	58.887%
LOW	1	0.214%
MODERATE	6	1.285%
MODIFIER	185	39.615%

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 0.405%

chromosome_number_variation 3 0.607%

conservative_inframe_deletion 6 1.215%

disruptive_inframe_deletion 1 0.202%

downstream_gene_variant 73 14.777%

duplication 4 0.81%

exon_loss_variant 6 1.215%

feature_ablation 67 13.563%

frameshift_variant 16 3.239%

gene_fusion 1 0.202%

intergenic_region 15 3.036%

splice_region_variant 9 1.822%

start_lost 9 1.822%

stop_lost 9 1.822%

transcript_ablation 176 35.628%

upstream_gene_variant 97 19.636%

Type (alphabetical order) Count Percent

CHROMOSOME 3 0.642%

DOWNSTREAM 73 15.632%

EXON 30 6.424%

GENE 71 15.203%

INTERGENIC 15 3.212%

TRANSCRIPT 178 38.116%

UPSTREAM 97 20.771%

Quality:

Insertions and deletions length:

	
		 Min 1  
		 Max 1  
		 Mean 1  
		 Median 1  
		 Standard deviation 0  
		 Values 1  
		 Count 19

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	22

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 30

AAC 40

AAG 86

AAT 70

ACA 42

ACC 55

ACG 49 1

ACT 17

AGA 9

AGC 46

AGG 17

AGT 19

ATA 26

ATC 83

ATG 60

ATT 68

CAA 23

CAC 25

CAG 59

CAT 20

CCA 17

CCC 28

CCG 57

CCT 21

CGA 11

CGC 64

CGG 23

CGT 28

CTA 11

CTC 32

CTG 80

CTT 65

GAA 87

GAC 82

GAG 69

GAT 97

GCA 65

GCC 97

GCG 102

GCT 67

GGA 40

GGC 161

GGG 34

GGT 37

GTA 19

GTC 46

GTG 47

GTT 53

TAA 2

TAC 24

TAT 40

TCA 15

TCC 29

TCG 41

TCT 14

TGA 7

TGC 17

TGG 32

TGT 5

TTA 12

TTC 61

TTG 37

TTT 50

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 331

C 22

D 179

E 156

F 111

G 272

H 45

I 177

K 116

L 237

M 60

N 110

P 123

Q 82

R 152

S 164

T 163 1

V 165

W 32

Y 64

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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0

		

		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 CRG1_fix_struct.snpEff_summary.csv -htmlStats CRG1_fix_struct.snpEff_summary.html brucella_suis_cita_364_fix CRG1_fix_struct.vcf
Warnings	32
Errors	3
Number of lines (input file)	22
Number of variants (before filter)	20
Number of not variants (i.e. reference equals alternative)	0
Number of variants processed (i.e. after filter and non-variants)	20
Number of known variants (i.e. non-empty ID)	20 ( 100% )
Number of multi-allelic VCF entries (i.e. more than two alleles)	0
Number of effects	467
Genome total length	3,328,972
Genome effective length	3,328,972
Variant rate	1 variant every 166,448 bases

	-	AGC
-
AAA	30
AAC	40
AAG	86
AAT	70
ACA	42
ACC	55
ACG	49	1
ACT	17
AGA	9
AGC	46
AGG	17
AGT	19
ATA	26
ATC	83
ATG	60
ATT	68
CAA	23
CAC	25
CAG	59
CAT	20
CCA	17
CCC	28
CCG	57
CCT	21
CGA	11
CGC	64
CGG	23
CGT	28
CTA	11
CTC	32
CTG	80
CTT	65
GAA	87
GAC	82
GAG	69
GAT	97
GCA	65
GCC	97
GCG	102
GCT	67
GGA	40
GGC	161
GGG	34
GGT	37
GTA	19
GTC	46
GTG	47
GTT	53
TAA	2
TAC	24
TAT	40
TCA	15
TCC	29
TCG	41
TCT	14
TGA	7
TGC	17
TGG	32
TGT	5
TTA	12
TTC	61
TTG	37
TTT	50

	-	S
*	9
-
A	331
C	22
D	179
E	156
F	111
G	272
H	45
I	177
K	116
L	237
M	60
N	110
P	123
Q	82
R	152
S	164
T	163	1
V	165
W	32
Y	64

	-	AGC
-
AAA	30
AAC	40
AAG	86
AAT	70
ACA	42
ACC	55
ACG	49	1
ACT	17
AGA	9
AGC	46
AGG	17
AGT	19
ATA	26
ATC	83
ATG	60
ATT	68
CAA	23
CAC	25
CAG	59
CAT	20
CCA	17
CCC	28
CCG	57
CCT	21
CGA	11
CGC	64
CGG	23
CGT	28
CTA	11
CTC	32
CTG	80
CTT	65
GAA	87
GAC	82
GAG	69
GAT	97
GCA	65
GCC	97
GCG	102
GCT	67
GGA	40
GGC	161
GGG	34
GGT	37
GTA	19
GTC	46
GTG	47
GTT	53
TAA	2
TAC	24
TAT	40
TCA	15
TCC	29
TCG	41
TCT	14
TGA	7
TGC	17
TGG	32
TGT	5
TTA	12
TTC	61
TTG	37
TTT	50

	-	S
*	9
-
A	331
C	22
D	179
E	156
F	111
G	272
H	45
I	177
K	116
L	237
M	60
N	110
P	123
Q	82
R	152
S	164
T	163	1
V	165
W	32
Y	64

	-	AGC
-
AAA	30
AAC	40
AAG	86
AAT	70
ACA	42
ACC	55
ACG	49	1
ACT	17
AGA	9
AGC	46
AGG	17
AGT	19
ATA	26
ATC	83
ATG	60
ATT	68
CAA	23
CAC	25
CAG	59
CAT	20
CCA	17
CCC	28
CCG	57
CCT	21
CGA	11
CGC	64
CGG	23
CGT	28
CTA	11
CTC	32
CTG	80
CTT	65
GAA	87
GAC	82
GAG	69
GAT	97
GCA	65
GCC	97
GCG	102
GCT	67
GGA	40
GGC	161
GGG	34
GGT	37
GTA	19
GTC	46
GTG	47
GTT	53
TAA	2
TAC	24
TAT	40
TCA	15
TCC	29
TCG	41
TCT	14
TGA	7
TGC	17
TGG	32
TGT	5
TTA	12
TTC	61
TTG	37
TTT	50

	-	S
*	9
-
A	331
C	22
D	179
E	156
F	111
G	272
H	45
I	177
K	116
L	237
M	60
N	110
P	123
Q	82
R	152
S	164
T	163	1
V	165
W	32
Y	64