RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0723699536:

Variant ID: vg0723699536 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 23699536
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

TCGGTGTGTTGTACTAATGTGCGAGTAGCGAGCTGGGAGGCAGAGAATTGCGCATCCAGGAGGATGGGTGGAATCACGTGATGTCATGAGTGACCAATTC[G/A]
CGAGCTTCGGGGAGCTCAAATTTTGACTTTTTGAGAAGCATATGGTGAAAATGTAGAAGAGCTGGATTTCTCAACTTCTGTTCTTTTGTTAATTTTTTGT

Reverse complement sequence

ACAAAAAATTAACAAAAGAACAGAAGTTGAGAAATCCAGCTCTTCTACATTTTCACCATATGCTTCTCAAAAAGTCAAAATTTGAGCTCCCCGAAGCTCG[C/T]
GAATTGGTCACTCATGACATCACGTGATTCCACCCATCCTCCTGGATGCGCAATTCTCTGCCTCCCAGCTCGCTACTCGCACATTAGTACAACACACCGA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.10%	1.30%	0.57%	0.00%	NA
All Indica	2759	96.80%	2.20%	0.94%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.00%	2.40%	1.68%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	92.10%	5.90%	2.04%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0723699536	G -> A	LOC_Os07g39560.1	upstream_gene_variant ; 4618.0bp to feature; MODIFIER	silent_mutation	Average:50.134; most accessible tissue: Callus, score: 69.008	N	N	N	N
vg0723699536	G -> A	LOC_Os07g39560.3	upstream_gene_variant ; 4618.0bp to feature; MODIFIER	silent_mutation	Average:50.134; most accessible tissue: Callus, score: 69.008	N	N	N	N
vg0723699536	G -> A	LOC_Os07g39550.1	downstream_gene_variant ; 3998.0bp to feature; MODIFIER	silent_mutation	Average:50.134; most accessible tissue: Callus, score: 69.008	N	N	N	N
vg0723699536	G -> A	LOC_Os07g39550-LOC_Os07g39560	intergenic_region ; MODIFIER	silent_mutation	Average:50.134; most accessible tissue: Callus, score: 69.008	N	N	N	N

Showing 1 to 4 of 4 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0723699536	NA	1.30E-07	mr1533	Ind_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
vg0723699536	NA	1.22E-08	mr1980	Ind_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
vg0723699536	NA	6.95E-10	mr1352_2	Ind_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
vg0723699536	NA	8.46E-15	mr1533_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
vg0723699536	4.57E-06	1.07E-10	mr1980_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

Showing 1 to 5 of 5 entries

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Search for Variation information by Variation ID:

Detailed information for vg0723699536:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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