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 CRG1_struct.snpEff_summary.csv -htmlStats CRG1_struct.snpEff_summary.html brucella_suis_cita_364 CRG1_struct.vcf
Warnings	69
Errors	2
Number of lines (input file)	25
Number of variants (before filter)	22
Number of not variants (i.e. reference equals alternative)	0
Number of variants processed (i.e. after filter and non-variants)	22
Number of known variants (i.e. non-empty ID)	22 ( 100% )
Number of multi-allelic VCF entries (i.e. more than two alleles)	0
Number of effects	433
Genome total length	3,328,972
Genome effective length	3,328,972
Variant rate	1 variant every 151,316 bases

Chromosome	Length	Variants	Variants rate
NZ_CP007697.1	1,927,594	17	113,387
NZ_CP007698.1	1,401,378	5	280,275
Total	3,328,972	22	151,316

Type	Total
SNP	0
MNP	0
INS	0
DEL	20
MIXED	0
INV	0
DUP	2
BND	0
INTERVAL	0
Total	22

Type (alphabetical order)		Count	Percent
HIGH		198	45.727%
MODERATE		6	1.386%
MODIFIER		229	52.887%

Type (alphabetical order)		Count	Percent

Missense / Silent ratio: 0

Type

Region

Type (alphabetical order)   Count Percent bidirectional_gene_fusion   6 1.325% chromosome_number_variation   2 0.442% conservative_inframe_deletion   7 1.545% disruptive_inframe_deletion   1 0.221% downstream_gene_variant   88 19.426% duplication   3 0.662% exon_loss_variant   4 0.883% feature_ablation   47 10.375% frameshift_variant   10 2.208% gene_fusion   7 1.545% intragenic_variant   7 1.545% intron_variant   21 4.636% splice_region_variant   6 1.325% start_lost   9 1.987% stop_lost   5 1.104% transcript_ablation   117 25.828% upstream_gene_variant   113 24.945%

Type (alphabetical order)   Count Percent CHROMOSOME   2 0.462% DOWNSTREAM   88 20.323% EXON   22 5.081% GENE   62 14.319% INTRON   21 4.85% TRANSCRIPT   125 28.868% UPSTREAM   113 26.097%

	A	C	G	T
A	0	0	0	0
C	0	0	0	0
G	0	0	0	0
T	0	0	0	0

	-	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	29
AAC	34
AAG	82
AAT	66
ACA	42
ACC	48
ACG	43										1
ACT	17
AGA	9
AGC	46
AGG	18
AGT	19
ATA	26
ATC	67
ATG	50
ATT	62
CAA	23
CAC	22
CAG	56
CAT	21
CCA	15
CCC	25
CCG	52
CCT	21
CGA	11
CGC	58
CGG	19
CGT	26
CTA	11
CTC	27
CTG	74
CTT	65
GAA	82
GAC	77
GAG	63
GAT	88
GCA	57
GCC	90
GCG	96
GCT	61
GGA	40
GGC	146
GGG	34
GGT	35
GTA	20
GTC	40
GTG	48
GTT	51
TAA	2
TAC	23
TAG	1
TAT	40
TCA	14
TCC	27
TCG	37
TCT	14
TGA	2
TGC	13
TGG	29
TGT	5
TTA	12
TTC	59
TTG	34
TTT	48

	*	-	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
*		5
-
A		304
C		18
D		165
E		145
F		107
G		255
H		43
I		155
K		111
L		223
M		50
N		100
P		113
Q		79
R		141
S		157
T		150																1
V		159
W		29
Y		63