RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0216649351:

Variant ID: vg0216649351 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 16649351
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

GCATGCACCCATTCGGACCAAAATAATTTTGGTAGATAAGTAGTAATCTCAGTCATAAACAGGCAGTCCCCAAAATTTAGGCTTAACTTCAGTTTCAATG[G/A]
CACATCACTACTAGAAAAAGCATTTTTCCCATAGTAGGGGTCTCATTTTCGCAGGCGGACATGACTCTTAAAGCCAAATGACCGTCACCAAAAATATAAA

Reverse complement sequence

TTTATATTTTTGGTGACGGTCATTTGGCTTTAAGAGTCATGTCCGCCTGCGAAAATGAGACCCCTACTATGGGAAAAATGCTTTTTCTAGTAGTGATGTG[C/T]
CATTGAAACTGAAGTTAAGCCTAAATTTTGGGGACTGCCTGTTTATGACTGAGATTACTACTTATCTACCAAAATTATTTTGGTCCGAATGGGTGCATGC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.60%	26.30%	0.02%	0.00%	NA
All Indica	2759	96.10%	3.90%	0.00%	0.00%	NA
All Japonica	1512	26.30%	73.60%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	91.00%	9.00%	0.00%	0.00%	NA
Indica III	913	95.00%	5.00%	0.00%	0.00%	NA
Indica Intermediate	786	97.70%	2.30%	0.00%	0.00%	NA
Temperate Japonica	767	4.70%	95.30%	0.00%	0.00%	NA
Tropical Japonica	504	61.70%	38.10%	0.20%	0.00%	NA
Japonica Intermediate	241	21.20%	78.80%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	0.00%	0.00%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0216649351	G -> A	LOC_Os02g28120.1	upstream_gene_variant ; 3113.0bp to feature; MODIFIER	silent_mutation	Average:59.272; most accessible tissue: Zhenshan97 flower, score: 70.756	N	N	N	N
vg0216649351	G -> A	LOC_Os02g28110-LOC_Os02g28120	intergenic_region ; MODIFIER	silent_mutation	Average:59.272; most accessible tissue: Zhenshan97 flower, score: 70.756	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0216649351	NA	2.76E-50	mr1016	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
vg0216649351	NA	2.12E-41	mr1017	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
vg0216649351	NA	1.92E-28	mr1022	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
vg0216649351	NA	5.30E-61	mr1023	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
vg0216649351	NA	2.84E-41	mr1055	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
vg0216649351	NA	1.96E-48	mr1079	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
vg0216649351	3.53E-11	3.46E-55	mr1089	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
vg0216649351	NA	3.03E-13	mr1089	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
vg0216649351	9.85E-18	1.08E-68	mr1093	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
vg0216649351	1.08E-08	2.42E-19	mr1093	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

Showing 1 to 10 of 88 entries

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Search for Variation information by Variation ID:

Detailed information for vg0216649351:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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