RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0220869926:

Variant ID: vg0220869926 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20869926
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, A: 0.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TATGTCCTGAAACATTATCATCAGCTGAATCATCACATATTCAAATGAAAAAAATAATTTTGTAAACCATGACAAAATGCTAACACACCTTGAAGTAACT[G/A]
TTATCAAACTTCAACCATTCAACTGTCCATGATTGCCCTCCAGGTTCACCAGGCCCATCCTTCTGTAGACCACAATAATAGAAGCCACCTTTAAATGTCA

Reverse complement sequence

TGACATTTAAAGGTGGCTTCTATTATTGTGGTCTACAGAAGGATGGGCCTGGTGAACCTGGAGGGCAATCATGGACAGTTGAATGGTTGAAGTTTGATAA[C/T]
AGTTACTTCAAGGTGTGTTAGCATTTTGTCATGGTTTACAAAATTATTTTTTTCATTTGAATATGTGATGATTCAGCTGATGATAATGTTTCAGGACATA

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	95.00%	5.00%	0.02%	0.00%	NA
All Indica	2759	97.40%	2.50%	0.04%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	40.50%	59.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	95.40%	4.60%	0.00%	0.00%	NA
Indica Intermediate	786	96.30%	3.60%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0220869926	G -> A	LOC_Os02g34810.1	synonymous_variant ; p.Asn287Asn; LOW	synonymous_codon	Average:52.152; most accessible tissue: Callus, score: 82.045	N	N	N	N

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220869926	NA	4.74E-06	mr1073	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
vg0220869926	NA	5.68E-06	mr1262	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
vg0220869926	NA	1.50E-18	mr1936	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
vg0220869926	7.04E-07	1.52E-08	mr1263_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
vg0220869926	NA	8.67E-06	mr1740_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

Showing 1 to 5 of 5 entries

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Search for Variation information by Variation ID:

Detailed information for vg0220869926:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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