RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0216594509:

Variant ID: vg0216594509 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 16594509
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CAGTATCAACCCACCAATTAGTAGACTAATTAACTGAAAAAACAGTTGCTAAATTACCATACTGCTTCCATCTCCAGTGTTGCCAATGGTCACATTAGCA[A/G]
ACTTAGAGGTCTGCCCTACAGGTGCCTTCATCCCCTTGCGTTGTGGACACTTCCTGGCCAGATGGCCAGGTTGACCACACACAAAGCAAGTCCTCTCATC

Reverse complement sequence

GATGAGAGGACTTGCTTTGTGTGTGGTCAACCTGGCCATCTGGCCAGGAAGTGTCCACAACGCAAGGGGATGAAGGCACCTGTAGGGCAGACCTCTAAGT[T/C]
TGCTAATGTGACCATTGGCAACACTGGAGATGGAAGCAGTATGGTAATTTAGCAACTGTTTTTTCAGTTAATTAGTCTACTAATTGGTGGGTTGATACTG

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	18.90%	11.40%	32.27%	37.52%	NA
All Indica	2759	7.00%	1.10%	46.68%	45.23%	NA
All Japonica	1512	37.20%	33.10%	7.28%	22.49%	NA
Aus	269	5.90%	0.40%	36.06%	57.62%	NA
Indica I	595	2.90%	1.00%	49.58%	46.55%	NA
Indica II	465	11.00%	0.90%	58.71%	29.46%	NA
Indica III	913	8.80%	0.90%	33.30%	57.06%	NA
Indica Intermediate	786	5.90%	1.40%	52.93%	39.82%	NA
Temperate Japonica	767	29.30%	59.30%	7.95%	3.39%	NA
Tropical Japonica	504	38.10%	1.60%	5.75%	54.56%	NA
Japonica Intermediate	241	60.20%	15.40%	8.30%	16.18%	NA
VI/Aromatic	96	94.80%	0.00%	3.12%	2.08%	NA
Intermediate	90	31.10%	7.80%	30.00%	31.11%	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
vg0216594509	A -> G	LOC_Os02g28020.1	missense_variant ; p.Phe238Ser; MODERATE	nonsynonymous_codon ; F238P	Average:42.393; most accessible tissue: Minghui63 young leaf, score: 71.254	unknown	unknown	DELETERIOUS	0.02
vg0216594509	A -> G	LOC_Os02g28020.1	missense_variant ; p.Phe238Ser; MODERATE	nonsynonymous_codon ; F238S	Average:42.393; most accessible tissue: Minghui63 young leaf, score: 71.254	unknown	unknown	TOLERATED	0.24
vg0216594509	A -> DEL	LOC_Os02g28020.1	N	frameshift_variant	Average:42.393; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N

Showing 1 to 3 of 3 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0216594509	NA	8.08E-15	Grain_length	All	YES	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
vg0216594509	NA	2.94E-06	mr1401	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
vg0216594509	NA	9.22E-07	mr1627_2	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
vg0216594509	NA	1.77E-07	mr1748_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 4 of 4 entries

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Search for Variation information by Variation ID:

Detailed information for vg0216594509:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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