RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1218287578:

Variant ID: vg1218287578 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18287578
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, T: 0.18, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

AGCAAATGCTACTCATTATAAGGATTTCGACAAAGCAAATTTGTTCATCACTAAAGCCGAAGTCAATAGGAGTACTATTATGAATAAATTCAGACCTCAG[G/T]
CTCGAGGACGTAGTTCTCCCATAAATAAAACCATGTGTCATATAACAATTCTACTAAATATAGTAAGAGCATAGTTGAAAATGGTATTCGGTGCACTTTC

Reverse complement sequence

GAAAGTGCACCGAATACCATTTTCAACTATGCTCTTACTATATTTAGTAGAATTGTTATATGACACATGGTTTTATTTATGGGAGAACTACGTCCTCGAG[C/A]
CTGAGGTCTGAATTTATTCATAATAGTACTCCTATTGACTTCGGCTTTAGTGATGAACAAATTTGCTTTGTCGAAATCCTTATAATGAGTAGCATTTGCT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.90%	38.40%	0.13%	0.59%	NA
All Indica	2759	40.80%	58.30%	0.07%	0.76%	NA
All Japonica	1512	99.00%	0.70%	0.07%	0.20%	NA
Aus	269	36.80%	62.80%	0.00%	0.37%	NA
Indica I	595	57.50%	41.70%	0.17%	0.67%	NA
Indica II	465	31.40%	67.70%	0.00%	0.86%	NA
Indica III	913	36.70%	62.50%	0.00%	0.77%	NA
Indica Intermediate	786	38.70%	60.40%	0.13%	0.76%	NA
Temperate Japonica	767	99.20%	0.70%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.00%	0.40%	NA
Japonica Intermediate	241	97.50%	2.10%	0.00%	0.41%	NA
VI/Aromatic	96	93.80%	5.20%	1.04%	0.00%	NA
Intermediate	90	73.30%	21.10%	2.22%	3.33%	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
vg1218287578	G -> DEL	LOC_Os12g30460.1	N	frameshift_variant	Average:32.315; most accessible tissue: Zhenshan97 young leaf, score: 53.969	N	N	N	N
vg1218287578	G -> T	LOC_Os12g30460.1	missense_variant ; p.Pro106Thr; MODERATE	nonsynonymous_codon ; P106T	Average:32.315; most accessible tissue: Zhenshan97 young leaf, score: 53.969	unknown	unknown	TOLERATED	0.26

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
vg1218287578	NA	2.40E-07	mr1013	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
vg1218287578	NA	3.59E-06	mr1014	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
vg1218287578	NA	1.34E-09	mr1031	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
vg1218287578	NA	5.68E-07	mr1034	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
vg1218287578	NA	4.23E-09	mr1056	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
vg1218287578	NA	6.32E-06	mr1098	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
vg1218287578	NA	1.17E-06	mr1398	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
vg1218287578	NA	9.35E-08	mr1559	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
vg1218287578	NA	9.99E-06	mr1631	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
vg1218287578	NA	2.30E-07	mr1761	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 10 of 15 entries

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Search for Variation information by Variation ID:

Detailed information for vg1218287578:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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