RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0323665466:

Variant ID: vg0323665466 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 23665466
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

AATTGAGGAAGTGATGGCCATTTCTCCACTCGAGCCCCCAGAGTCTATTTTTGATGAATCCATCGAAGAATTTAATGAAGGGGAGGATGAAACTGGAGAA[C/A]
CGATGGATCAGCCAAAAACGGATCTGTCGTCACGAGCCCCAATTGAGCTAAAGCCCTTACCTTCAGGCCTACGTTATGCATTTCTGAACGGCGATGCGGA

Reverse complement sequence

TCCGCATCGCCGTTCAGAAATGCATAACGTAGGCCTGAAGGTAAGGGCTTTAGCTCAATTGGGGCTCGTGACGACAGATCCGTTTTTGGCTGATCCATCG[G/T]
TTCTCCAGTTTCATCCTCCCCTTCATTAAATTCTTCGATGGATTCATCAAAAATAGACTCTGGGGGCTCGAGTGGAGAAATGGCCATCACTTCCTCAATT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.20%	10.60%	1.23%	0.00%	NA
All Indica	2759	99.80%	0.10%	0.07%	0.00%	NA
All Japonica	1512	66.50%	30.20%	3.31%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.40%	0.13%	0.00%	NA
Temperate Japonica	767	43.50%	52.20%	4.30%	0.00%	NA
Tropical Japonica	504	92.30%	5.80%	1.98%	0.00%	NA
Japonica Intermediate	241	85.50%	11.60%	2.90%	0.00%	NA
VI/Aromatic	96	64.60%	33.30%	2.08%	0.00%	NA
Intermediate	90	87.80%	8.90%	3.33%	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
vg0323665466	C -> A	LOC_Os03g42530.1	missense_variant ; p.Pro433Thr; MODERATE	nonsynonymous_codon ; P433T	Average:42.731; most accessible tissue: Minghui63 young leaf, score: 62.741	unknown	unknown	TOLERATED	1.00

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0323665466	NA	5.54E-12	Heading_date	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0323665466	NA	2.17E-10	Heading_date	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0323665466	6.40E-08	NA	mr1210	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
vg0323665466	2.98E-07	NA	mr1305	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
vg0323665466	NA	8.11E-06	mr1548	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
vg0323665466	8.18E-08	NA	mr1586	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
vg0323665466	3.25E-08	NA	mr1765	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
vg0323665466	8.42E-07	7.70E-06	mr1765	Jap_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
vg0323665466	NA	2.74E-11	mr1902	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
vg0323665466	NA	8.30E-06	mr1902	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 24 entries

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Search for Variation information by Variation ID:

Detailed information for vg0323665466:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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