Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0818644712:

Variant ID: vg0818644712 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18644712
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCATACGATGGAGGTATTGTGTGCGTATGGATGCGGAGTCGAATTTGGAAGGAGTGCAAATTTGGTACGATTGGTTATGTAAAGTTTCTTTCTTGTACTA[G/C]
AGGGTTTCCTAAGGTGTTTAAGACTCTTCGTATGAGTTTGGTTCATGGCTTTAGGCTGCCTACCTCATGTATAAATAGAGGGGGAGCGTGAGGCTTCCCG

Reverse complement sequence

CGGGAAGCCTCACGCTCCCCCTCTATTTATACATGAGGTAGGCAGCCTAAAGCCATGAACCAAACTCATACGAAGAGTCTTAAACACCTTAGGAAACCCT[C/G]
TAGTACAAGAAAGAAACTTTACATAACCAATCGTACCAAATTTGCACTCCTTCCAAATTCGACTCCGCATCCATACGCACACAATACCTCCATCGTATGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.70%	1.90%	6.12%	7.26%	NA
All Indica	2759	82.20%	0.40%	5.87%	11.45%	NA
All Japonica	1512	88.30%	4.70%	6.81%	0.20%	NA
Aus	269	85.10%	0.00%	7.06%	7.81%	NA
Indica I	595	71.80%	0.80%	6.39%	21.01%	NA
Indica II	465	74.60%	0.00%	14.62%	10.75%	NA
Indica III	913	89.30%	0.00%	1.64%	9.09%	NA
Indica Intermediate	786	86.50%	0.90%	5.22%	7.38%	NA
Temperate Japonica	767	79.10%	8.90%	11.73%	0.26%	NA
Tropical Japonica	504	99.60%	0.00%	0.20%	0.20%	NA
Japonica Intermediate	241	93.80%	1.20%	4.98%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	6.70%	5.56%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818644712	G -> C	LOC_Os08g30300.1	downstream_gene_variant ; 2488.0bp to feature; MODIFIER	silent_mutation	Average:25.75; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	N	N	N	N
vg0818644712	G -> C	LOC_Os08g30300-LOC_Os08g30310	intergenic_region ; MODIFIER	silent_mutation	Average:25.75; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	N	N	N	N
vg0818644712	G -> DEL	N	N	silent_mutation	Average:25.75; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818644712	9.21E-06	8.58E-08	mr1946_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0818644712	9.21E-06	8.58E-08	mr1948_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0818644712	NA	1.06E-06	mr1977_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251