RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0919855604:

Variant ID: vg0919855604 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 19855604
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGGAAAGTCATAATATGCTTTTCCCTTGGACATCGAGAGGCTGAGCTCTTCGATCCTTGGTGTAACAGCAATTTGAAGCCATCTTTCGAGGTAACTGC[G/A]
TGCTTTGGTACTGAAGAGACCATTGAACTCAATCGTAAGAGCCTTCACACCAATGCCTGAGTGTTTTTCCATAACGCGATCAATTTTTCTGATGAAATCC

Reverse complement sequence

GGATTTCATCAGAAAAATTGATCGCGTTATGGAAAAACACTCAGGCATTGGTGTGAAGGCTCTTACGATTGAGTTCAATGGTCTCTTCAGTACCAAAGCA[C/T]
GCAGTTACCTCGAAAGATGGCTTCAAATTGCTGTTACACCAAGGATCGAAGAGCTCAGCCTCTCGATGTCCAAGGGAAAAGCATATTATGACTTTCCTTG

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	89.80%	9.70%	0.51%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.00%	0.00%	NA
All Japonica	1512	71.30%	27.10%	1.59%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.20%	1.80%	0.00%	0.00%	NA
Temperate Japonica	767	49.90%	47.10%	3.00%	0.00%	NA
Tropical Japonica	504	96.20%	3.60%	0.20%	0.00%	NA
Japonica Intermediate	241	87.10%	12.90%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg0919855604	G -> A	LOC_Os09g33620.1	missense_variant ; p.Arg133Cys; MODERATE	nonsynonymous_codon ; R133C	Average:45.899; most accessible tissue: Minghui63 root, score: 72.958	unknown	unknown	TOLERATED	0.19

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
vg0919855604	NA	2.63E-08	mr1002	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
vg0919855604	NA	7.68E-07	mr1002	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
vg0919855604	NA	4.27E-06	mr1069	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
vg0919855604	NA	8.94E-06	mr1077	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
vg0919855604	4.71E-06	NA	mr1137	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
vg0919855604	NA	7.40E-13	mr1137	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
vg0919855604	NA	9.29E-07	mr1164	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
vg0919855604	6.18E-07	4.05E-16	mr1182	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
vg0919855604	NA	8.67E-09	mr1182	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
vg0919855604	NA	2.50E-07	mr1183	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

Showing 1 to 10 of 40 entries

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Search for Variation information by Variation ID:

Detailed information for vg0919855604:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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