RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0420837342:

Variant ID: vg0420837342 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20837342
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.52, A: 0.48, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

GCTACCTAAGCAACTCTACCATAGCAGTGAAAAGGCTTGATGGTGCCCGTCAAGGAGAGAAGCAGTTCAGGGCTGAAGTGAATTCAATTGGAATCATCCA[A/G]
CGTATTAACTTAGTTAAATTGGTCGGGTTTTGTTGCGAAGGTGATAATAGGTTACTTGTGTATGAATACATGCCAAACAGCTCCCTTGATGTGTGTTTAT

Reverse complement sequence

ATAAACACACATCAAGGGAGCTGTTTGGCATGTATTCATACACAAGTAACCTATTATCACCTTCGCAACAAAACCCGACCAATTTAACTAAGTTAATACG[T/C]
TGGATGATTCCAATTGAATTCACTTCAGCCCTGAACTGCTTCTCTCCTTGACGGGCACCATCAAGCCTTTTCACTGCTATGGTAGAGTTGCTTAGGTAGC

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	69.10%	30.80%	0.08%	0.00%	NA
All Indica	2759	93.20%	6.70%	0.04%	0.00%	NA
All Japonica	1512	35.60%	64.30%	0.07%	0.00%	NA
Aus	269	23.80%	76.20%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	94.80%	5.20%	0.00%	0.00%	NA
Indica III	913	91.90%	8.00%	0.11%	0.00%	NA
Indica Intermediate	786	88.90%	11.10%	0.00%	0.00%	NA
Temperate Japonica	767	18.00%	82.00%	0.00%	0.00%	NA
Tropical Japonica	504	63.50%	36.30%	0.20%	0.00%	NA
Japonica Intermediate	241	33.60%	66.40%	0.00%	0.00%	NA
VI/Aromatic	96	45.80%	54.20%	0.00%	0.00%	NA
Intermediate	90	54.40%	43.30%	2.22%	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
vg0420837342	A -> G	LOC_Os04g34410.1	synonymous_variant ; p.Gln574Gln; LOW	synonymous_codon	Average:33.73; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

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
vg0420837342	NA	3.53E-07	mr1030	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
vg0420837342	NA	7.07E-13	mr1031	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
vg0420837342	NA	1.13E-11	mr1045	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
vg0420837342	NA	4.63E-08	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
vg0420837342	NA	3.93E-13	mr1056	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
vg0420837342	NA	2.95E-06	mr1118	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
vg0420837342	NA	5.63E-17	mr1147	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
vg0420837342	NA	7.48E-08	mr1157	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
vg0420837342	NA	1.12E-07	mr1162	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
vg0420837342	NA	2.34E-21	mr1179	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 54 entries

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Search for Variation information by Variation ID:

Detailed information for vg0420837342:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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