Search for Variation information by Variation ID:

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

Detailed information for vg0529433705:

Variant ID: vg0529433705 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 29433705
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTTGTAACCTGTGTTTTCCATCATATAATCCCACATCAACTGGATTAGGGCTATTACCTATCAAGGGGCCTGAACCAGTATAATCTTTGTCTTTGATC[T/C]
ACTTGATGTCGTATTACGTAGATCCTTGTACCAACGTACCCTAATACCCTCTATATCCGATCTATGGGTATCACCCATCGATAGTGGCGCGCCAGGTAGG

Reverse complement sequence

CCTACCTGGCGCGCCACTATCGATGGGTGATACCCATAGATCGGATATAGAGGGTATTAGGGTACGTTGGTACAAGGATCTACGTAATACGACATCAAGT[A/G]
GATCAAAGACAAAGATTATACTGGTTCAGGCCCCTTGATAGGTAATAGCCCTAATCCAGTTGATGTGGGATTATATGATGGAAAACACAGGTTACAAAGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.20%	28.90%	26.89%	0.00%	NA
All Indica	2759	17.90%	39.10%	42.99%	0.00%	NA
All Japonica	1512	95.60%	3.30%	1.12%	0.00%	NA
Aus	269	5.90%	78.80%	15.24%	0.00%	NA
Indica I	595	14.60%	36.30%	49.08%	0.00%	NA
Indica II	465	30.30%	27.70%	41.94%	0.00%	NA
Indica III	913	13.70%	48.10%	38.23%	0.00%	NA
Indica Intermediate	786	17.80%	37.70%	44.53%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	87.70%	9.30%	2.98%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	88.50%	2.10%	9.38%	0.00%	NA
Intermediate	90	54.40%	25.60%	20.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0529433705	T -> C	LOC_Os05g51300.1	upstream_gene_variant ; 3012.0bp to feature; MODIFIER	silent_mutation	Average:37.372; most accessible tissue: Minghui63 young leaf, score: 53.016	N	N	N	N
vg0529433705	T -> C	LOC_Os05g51320.1	upstream_gene_variant ; 2527.0bp to feature; MODIFIER	silent_mutation	Average:37.372; most accessible tissue: Minghui63 young leaf, score: 53.016	N	N	N	N
vg0529433705	T -> C	LOC_Os05g51310.1	intron_variant ; MODIFIER	silent_mutation	Average:37.372; most accessible tissue: Minghui63 young leaf, score: 53.016	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0529433705	NA	8.31E-06	mr1569	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
vg0529433705	4.27E-06	NA	mr1661	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