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 CRG2_fix_struct.snpEff_summary.csv -htmlStats CRG2_fix_struct.snpEff_summary.html brucella_suis_cita_364_fix CRG2_fix_struct.vcf
Warnings	31
Errors	3
Number of lines (input file)	18
Number of variants (before filter)	16
Number of not variants (i.e. reference equals alternative)	0
Number of variants processed (i.e. after filter and non-variants)	16
Number of known variants (i.e. non-empty ID)	16 ( 100% )
Number of multi-allelic VCF entries (i.e. more than two alleles)	0
Number of effects	420
Genome total length	3,328,972
Genome effective length	3,328,972
Variant rate	1 variant every 208,060 bases

Chromosome	Length	Variants	Variants rate
OOAJICEE_1	1,927,594	12	160,632
OOAJICEE_2	1,401,378	4	350,344
Total	3,328,972	16	208,060

Type	Total
SNP	0
MNP	0
INS	0
DEL	15
MIXED	0
INV	0
DUP	1
BND	0
INTERVAL	0
Total	16

Type (alphabetical order)		Count	Percent
HIGH		272	64.762%
LOW		1	0.238%
MODERATE		5	1.19%
MODIFIER		142	33.81%

Type (alphabetical order)		Count	Percent

Missense / Silent ratio: 0

Type

Region

Type (alphabetical order)   Count Percent bidirectional_gene_fusion   2 0.449% chromosome_number_variation   3 0.674% conservative_inframe_deletion   5 1.124% downstream_gene_variant   60 13.483% duplication   4 0.899% exon_loss_variant   6 1.348% feature_ablation   67 15.056% frameshift_variant   15 3.371% gene_fusion   1 0.225% intergenic_region   11 2.472% splice_region_variant   9 2.022% start_lost   7 1.573% stop_lost   9 2.022% transcript_ablation   175 39.326% upstream_gene_variant   71 15.955%

Type (alphabetical order)   Count Percent CHROMOSOME   3 0.714% DOWNSTREAM   60 14.286% EXON   27 6.429% GENE   71 16.905% INTERGENIC   11 2.619% TRANSCRIPT   177 42.143% UPSTREAM   71 16.905%

	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	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	60
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		134
S		84
T		74
V		107
W		27
Y		50