RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0212369213:

Variant ID: vg0212369213 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 12369213
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

TGACAATGGCTGTTATAATTCAGAGTGTGCTAGATGTAACCGGGTTGGAATTTAAATTATTCATGGATTTCCTGCGGAGTCTCAGTATATTTGGGGATTC[C/T]
GCTCCTCGAGAGTCGTTCCAGGAATTGATTGAAATCATTCAAGCACAAGCTGATCTTGATGCACAATTCAATGTAAGTATGTTCTTTGAATGTTCCTGGA

Reverse complement sequence

TCCAGGAACATTCAAAGAACATACTTACATTGAATTGTGCATCAAGATCAGCTTGTGCTTGAATGATTTCAATCAATTCCTGGAACGACTCTCGAGGAGC[G/A]
GAATCCCCAAATATACTGAGACTCCGCAGGAAATCCATGAATAATTTAAATTCCAACCCGGTTACATCTAGCACACTCTGAATTATAACAGCCATTGTCA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.40%	9.60%	5.01%	0.00%	NA
All Indica	2759	76.30%	15.60%	8.12%	0.00%	NA
All Japonica	1512	99.20%	0.50%	0.26%	0.00%	NA
Aus	269	98.10%	0.00%	1.86%	0.00%	NA
Indica I	595	59.70%	23.90%	16.47%	0.00%	NA
Indica II	465	60.60%	29.90%	9.46%	0.00%	NA
Indica III	913	99.60%	0.10%	0.33%	0.00%	NA
Indica Intermediate	786	71.00%	19.00%	10.05%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.40%	0.00%	NA
Japonica Intermediate	241	98.30%	0.80%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	14.40%	4.44%	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
vg0212369213	C -> T	LOC_Os02g20930.1	synonymous_variant ; p.Ser216Ser; LOW	synonymous_codon	Average:50.404; most accessible tissue: Minghui63 flag leaf, score: 67.635	N	N	N	N

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
vg0212369213	1.08E-06	NA	mr1089	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
vg0212369213	3.41E-07	7.82E-10	mr1089	Ind_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
vg0212369213	NA	6.98E-09	mr1093	Ind_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
vg0212369213	3.16E-09	NA	mr1109	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
vg0212369213	1.16E-07	1.54E-16	mr1109	Ind_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
vg0212369213	1.25E-07	NA	mr1129	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
vg0212369213	1.25E-06	2.36E-15	mr1129	Ind_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
vg0212369213	1.81E-07	NA	mr1235	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
vg0212369213	1.57E-07	2.84E-10	mr1235	Ind_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
vg0212369213	NA	1.43E-08	mr1236	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 56 entries

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Search for Variation information by Variation ID:

Detailed information for vg0212369213:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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