Search for Variation information by Variation ID:

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

Detailed information for vg1205658688:

Variant ID: vg1205658688 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5658688
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.66, C: 0.32, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGATTAAAGGTCTAGCGATGGCTTCAGCTCCACTCCCACAGGCAGCTCAACTGGGGTATAAGCCAAACGTCTTCTCCTTCTGGATCCTTTCTCTTCAA[C/T]
TAAGGTTGATTGATTATTGCAAGGTGAGCATATGACATACTCAACAAGCCACACAGCAAATATGCAAGTGTACAAGAATACCAAAGGATAGCATAATATA

Reverse complement sequence

TATATTATGCTATCCTTTGGTATTCTTGTACACTTGCATATTTGCTGTGTGGCTTGTTGAGTATGTCATATGCTCACCTTGCAATAATCAATCAACCTTA[G/A]
TTGAAGAGAAAGGATCCAGAAGGAGAAGACGTTTGGCTTATACCCCAGTTGAGCTGCCTGTGGGAGTGGAGCTGAAGCCATCGCTAGACCTTTAATCCAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.20%	7.90%	42.32%	0.55%	NA
All Indica	2759	19.80%	13.10%	66.15%	0.94%	NA
All Japonica	1512	96.60%	0.30%	3.11%	0.00%	NA
Aus	269	59.50%	1.50%	39.03%	0.00%	NA
Indica I	595	21.80%	16.80%	61.18%	0.17%	NA
Indica II	465	13.50%	15.50%	69.68%	1.29%	NA
Indica III	913	22.60%	9.60%	66.27%	1.53%	NA
Indica Intermediate	786	18.70%	13.00%	67.68%	0.64%	NA
Temperate Japonica	767	95.40%	0.30%	4.30%	0.00%	NA
Tropical Japonica	504	97.40%	0.40%	2.18%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	1.24%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	73.30%	2.20%	24.44%	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
vg1205658688	C -> DEL	N	N	silent_mutation	Average:32.533; most accessible tissue: Minghui63 flag leaf, score: 42.823	N	N	N	N
vg1205658688	C -> T	LOC_Os12g10604.1	downstream_gene_variant ; 1514.0bp to feature; MODIFIER	silent_mutation	Average:32.533; most accessible tissue: Minghui63 flag leaf, score: 42.823	N	N	N	N
vg1205658688	C -> T	LOC_Os12g10620.1	downstream_gene_variant ; 3545.0bp to feature; MODIFIER	silent_mutation	Average:32.533; most accessible tissue: Minghui63 flag leaf, score: 42.823	N	N	N	N
vg1205658688	C -> T	LOC_Os12g10610.1	intron_variant ; MODIFIER	silent_mutation	Average:32.533; most accessible tissue: Minghui63 flag leaf, score: 42.823	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205658688	NA	3.33E-07	mr1604_2	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
vg1205658688	NA	1.66E-06	mr1892_2	Ind_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