RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0206231967:

Variant ID: vg0206231967 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6231967
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

AGCAGGGCTTCTCTATCAGTGTCTGTGTCATCACTGATTGCTAATGGCAGGGAACTTGAGAAGATGAAGACAGCCAAGAGAGGAATGAGTTTTGGGCAGG[A/G]
AGCAAACAAGCGGATCATTTTGCTGTTGGTGCTGAGGGCAGTGAGGCTTGCTATTTTGCTTATGGCTAATATGTAGGAGGAGGCACGCACTTGCCTTATA

Reverse complement sequence

TATAAGGCAAGTGCGTGCCTCCTCCTACATATTAGCCATAAGCAAAATAGCAAGCCTCACTGCCCTCAGCACCAACAGCAAAATGATCCGCTTGTTTGCT[T/C]
CCTGCCCAAAACTCATTCCTCTCTTGGCTGTCTTCATCTTCTCAAGTTCCCTGCCATTAGCAATCAGTGATGACACAGACACTGATAGAGAAGCCCTGCT

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	44.60%	40.40%	0.13%	14.85%	NA
All Indica	2759	62.20%	12.60%	0.14%	25.05%	NA
All Japonica	1512	2.20%	97.60%	0.00%	0.26%	NA
Aus	269	97.80%	0.70%	0.37%	1.12%	NA
Indica I	595	48.70%	2.20%	0.50%	48.57%	NA
Indica II	465	49.70%	26.70%	0.22%	23.44%	NA
Indica III	913	72.20%	14.20%	0.00%	13.58%	NA
Indica Intermediate	786	68.20%	10.30%	0.00%	21.50%	NA
Temperate Japonica	767	1.80%	97.70%	0.00%	0.52%	NA
Tropical Japonica	504	1.60%	98.40%	0.00%	0.00%	NA
Japonica Intermediate	241	4.60%	95.40%	0.00%	0.00%	NA
VI/Aromatic	96	58.30%	41.70%	0.00%	0.00%	NA
Intermediate	90	44.40%	50.00%	1.11%	4.44%	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
vg0206231967	A -> G	LOC_Os02g12010.1	missense_variant ; p.Ser7Pro; MODERATE	nonsynonymous_codon ; S7P	Average:44.458; most accessible tissue: Callus, score: 92.337	benign	1.394	TOLERATED	0.26
vg0206231967	A -> DEL	LOC_Os02g12010.1	N	frameshift_variant	Average:44.458; most accessible tissue: Callus, score: 92.337	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
vg0206231967	3.39E-07	3.83E-19	mr1170	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
vg0206231967	6.89E-06	2.13E-06	mr1170	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
vg0206231967	NA	1.68E-09	mr1301	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
vg0206231967	NA	3.12E-10	mr1410	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
vg0206231967	NA	5.11E-10	mr1714	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
vg0206231967	NA	1.80E-08	mr1030_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
vg0206231967	1.93E-09	3.86E-16	mr1170_2	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
vg0206231967	6.92E-08	1.06E-08	mr1170_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
vg0206231967	NA	4.29E-07	mr1408_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
vg0206231967	NA	5.30E-06	mr1555_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 10 of 15 entries

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Search for Variation information by Variation ID:

Detailed information for vg0206231967:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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