RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0233733433:

Variant ID: vg0233733433 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 33733433
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.02, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GGCATCATCCAATGAATTGTTGGAGAAGATTACCCAGCAGCTTTTGAGCGACTCACATGTTGCACCAGCCTCAGATGAGAAACGGGTGATGGCAAGGGTT[G/T]
GTTCTCTTCTTTCTCTGCTTCAGAAAGACGCAGTGCCAGCCAATTTACCCAAGTTTGAGCCCAATGACAGCGGCAAGATTGGTGTAGTTGAAGTGGGAAT

Reverse complement sequence

ATTCCCACTTCAACTACACCAATCTTGCCGCTGTCATTGGGCTCAAACTTGGGTAAATTGGCTGGCACTGCGTCTTTCTGAAGCAGAGAAAGAAGAGAAC[C/A]
AACCCTTGCCATCACCCGTTTCTCATCTGAGGCTGGTGCAACATGTGAGTCGCTCAAAAGCTGCTGGGTAATCTTCTCCAACAATTCATTGGATGATGCC

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	94.20%	5.80%	0.00%	0.00%	NA
All Indica	2759	96.90%	3.10%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	33.10%	66.90%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	95.20%	4.80%	0.00%	0.00%	NA
Indica Intermediate	786	95.90%	4.10%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0233733433	G -> T	LOC_Os02g55070.1	missense_variant ; p.Gly451Cys; MODERATE	nonsynonymous_codon ; G451C	Average:69.448; most accessible tissue: Callus, score: 82.572	unknown	unknown	DELETERIOUS	0.00

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
vg0233733433	NA	3.36E-06	mr1029	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
vg0233733433	NA	4.16E-07	mr1053	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
vg0233733433	NA	6.66E-06	mr1189	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
vg0233733433	NA	3.10E-06	mr1207	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
vg0233733433	4.03E-06	7.94E-13	mr1471	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
vg0233733433	NA	2.16E-06	mr1596	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
vg0233733433	NA	3.86E-06	mr1625	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
vg0233733433	7.60E-06	6.09E-12	mr1722	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
vg0233733433	NA	4.83E-07	mr1735	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
vg0233733433	NA	7.20E-06	mr1787	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 14 entries

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Search for Variation information by Variation ID:

Detailed information for vg0233733433:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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