RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0529371054:

Variant ID: vg0529371054 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 29371054
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GTATCTCATGAGCCTGTTCGACTACAGAACGGTTGTTAGCCATCTTGTAGTCATGAAACTGCTCCATGATATACAGATCATTGCTAGCATCAGTAGCACC[A/G]
AATTTAGTATTCAGTGCATCCCACAATTCCTTAGCGTCGGTCATATGCATATACACCTCGACAAGACGATCGCCAAGCACGCTAAGAATGCATCCCATAA

Reverse complement sequence

TTATGGGATGCATTCTTAGCGTGCTTGGCGATCGTCTTGTCGAGGTGTATATGCATATGACCGACGCTAAGGAATTGTGGGATGCACTGAATACTAAATT[T/C]
GGTGCTACTGATGCTAGCAATGATCTGTATATCATGGAGCAGTTTCATGACTACAAGATGGCTAACAACCGTTCTGTAGTCGAACAGGCTCATGAGATAC

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	63.50%	36.20%	0.25%	0.00%	NA
All Indica	2759	94.30%	5.40%	0.36%	0.00%	NA
All Japonica	1512	4.80%	95.20%	0.00%	0.00%	NA
Aus	269	97.00%	2.60%	0.37%	0.00%	NA
Indica I	595	98.20%	1.50%	0.34%	0.00%	NA
Indica II	465	83.40%	16.10%	0.43%	0.00%	NA
Indica III	913	97.70%	1.90%	0.44%	0.00%	NA
Indica Intermediate	786	93.80%	6.00%	0.25%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	13.10%	86.90%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	16.70%	83.30%	0.00%	0.00%	NA
Intermediate	90	57.80%	41.10%	1.11%	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
vg0529371054	A -> G	LOC_Os05g51200.1	synonymous_variant ; p.Phe94Phe; LOW	synonymous_codon	Average:18.383; most accessible tissue: Zhenshan97 panicle, score: 24.575	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
vg0529371054	2.02E-06	NA	mr1161	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
vg0529371054	NA	2.36E-22	mr1548	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
vg0529371054	NA	2.37E-20	mr1588	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
vg0529371054	NA	9.61E-15	mr1162_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
vg0529371054	NA	3.50E-07	mr1478_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
vg0529371054	NA	1.09E-28	mr1588_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
vg0529371054	NA	2.60E-08	mr1588_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
vg0529371054	NA	8.70E-17	mr1712_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
vg0529371054	NA	2.35E-07	mr1749_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
vg0529371054	NA	1.11E-10	mr1893_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 10 entries

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Search for Variation information by Variation ID:

Detailed information for vg0529371054:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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