RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1125246293:

Variant ID: vg1125246293 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25246293
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:

CGGTGAAGGCTTTTTTTTACTGGATGATCATTGTTCACAGTTCATGGCGCGGATTGCTGATGCGAAGAGATCAATCTTCCATCTTCTCTTTGCTCAAGCA[G/T]
TGTTTGATTCTGCAAGCTTCAATGGCCCGAGGTGCAATGGCGGCTGCTCACATGAAACCATCGTCGGCATTGTCCAAGCAGTGTTCAAGCACCATGCGTA

Reverse complement sequence

TACGCATGGTGCTTGAACACTGCTTGGACAATGCCGACGATGGTTTCATGTGAGCAGCCGCCATTGCACCTCGGGCCATTGAAGCTTGCAGAATCAAACA[C/A]
TGCTTGAGCAAAGAGAAGATGGAAGATTGATCTCTTCGCATCAGCAATCCGCGCCATGAACTGTGAACAATGATCATCCAGTAAAAAAAAGCCTTCACCG

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	94.30%	5.70%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	83.00%	17.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	71.20%	28.80%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	88.00%	12.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg1125246293	G -> T	LOC_Os11g41990.1	3_prime_UTR_variant ; 48.0bp to feature; MODIFIER	silent_mutation	Average:71.989; most accessible tissue: Callus, score: 82.227	N	N	N	N
vg1125246293	G -> T	LOC_Os11g41990.2	3_prime_UTR_variant ; 48.0bp to feature; MODIFIER	silent_mutation	Average:71.989; most accessible tissue: Callus, score: 82.227	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125246293	1.36E-08	NA	mr1484	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
vg1125246293	2.44E-06	NA	mr1484	Jap_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
vg1125246293	4.41E-11	1.30E-13	mr1530	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
vg1125246293	6.47E-07	1.08E-09	mr1530	Jap_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
vg1125246293	1.42E-10	NA	mr1745	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
vg1125246293	8.36E-07	NA	mr1745	Jap_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
vg1125246293	4.31E-06	NA	mr1926	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
vg1125246293	NA	6.78E-09	mr1002_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
vg1125246293	2.00E-07	NA	mr1484_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
vg1125246293	2.40E-11	NA	mr1530_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 13 entries

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Search for Variation information by Variation ID:

Detailed information for vg1125246293:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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