RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0727660294:

Variant ID: vg0727660294 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27660294
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGGGACAAAAGTTCACTGCGTGCTCTGTGCGATAAAAAAGCACAAGAATCTCTGTATGTGCTTTCCTCTAAGTAGAACACTTATACTAATCTTGGCCT[G/T]
CCTAGTAACTCTGTTATAAATGTCTGAACAGATCTGATGAGGAGAGAGAAACATGGGGCTTCCTAAGGGTAATGTTTGAGGATGGGGATGCTGCCAGGAC

Reverse complement sequence

GTCCTGGCAGCATCCCCATCCTCAAACATTACCCTTAGGAAGCCCCATGTTTCTCTCTCCTCATCAGATCTGTTCAGACATTTATAACAGAGTTACTAGG[C/A]
AGGCCAAGATTAGTATAAGTGTTCTACTTAGAGGAAAGCACATACAGAGATTCTTGTGCTTTTTTATCGCACAGAGCACGCAGTGAACTTTTGTCCCCAT

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	84.50%	15.50%	0.02%	0.00%	NA
All Indica	2759	98.90%	1.10%	0.00%	0.00%	NA
All Japonica	1512	54.80%	45.20%	0.07%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	97.20%	2.80%	0.00%	0.00%	NA
Temperate Japonica	767	85.80%	14.10%	0.13%	0.00%	NA
Tropical Japonica	504	18.70%	81.30%	0.00%	0.00%	NA
Japonica Intermediate	241	31.50%	68.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg0727660294	G -> T	LOC_Os07g46370.1	intron_variant ; MODIFIER	silent_mutation	Average:71.949; most accessible tissue: Callus, score: 89.955	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
vg0727660294	5.10E-06	NA	mr1348	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
vg0727660294	NA	8.78E-07	mr1408	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
vg0727660294	NA	5.21E-09	mr1637	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
vg0727660294	NA	8.96E-06	mr1749	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
vg0727660294	NA	2.02E-09	mr1398_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
vg0727660294	NA	8.34E-08	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
vg0727660294	NA	1.44E-13	mr1552_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
vg0727660294	NA	1.48E-06	mr1691_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
vg0727660294	NA	4.44E-09	mr1851_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
vg0727660294	NA	5.22E-13	mr1864_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 12 entries

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Search for Variation information by Variation ID:

Detailed information for vg0727660294:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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