RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0610114031:

Variant ID: vg0610114031 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10114031
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTTTACCAAATAAAAAACTATAACCATCCCATACCACAAATCAAACACACAACTGGAACCATCCCATCCTAAAAAACTGGGATGGGTCTAACCCATCC[C/T]
ACTTGGTCCCCAAACCAAACACACCCTAGAATGGCATATAACGATACTCCCTCCGTTTCAAAATATTTGACACTGTTGACTTTTTAAGTACATGTTTGAC

Reverse complement sequence

GTCAAACATGTACTTAAAAAGTCAACAGTGTCAAATATTTTGAAACGGAGGGAGTATCGTTATATGCCATTCTAGGGTGTGTTTGGTTTGGGGACCAAGT[G/A]
GGATGGGTTAGACCCATCCCAGTTTTTTAGGATGGGATGGTTCCAGTTGTGTGTTTGATTTGTGGTATGGGATGGTTATAGTTTTTTATTTGGTAAAAGG

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	74.70%	24.40%	0.30%	0.59%	NA
All Indica	2759	62.10%	36.50%	0.47%	1.01%	NA
All Japonica	1512	93.30%	6.70%	0.00%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	83.90%	15.00%	0.50%	0.67%	NA
Indica II	465	17.60%	79.10%	0.43%	2.80%	NA
Indica III	913	73.40%	26.10%	0.44%	0.11%	NA
Indica Intermediate	786	58.70%	39.60%	0.51%	1.27%	NA
Temperate Japonica	767	94.90%	5.10%	0.00%	0.00%	NA
Tropical Japonica	504	90.30%	9.70%	0.00%	0.00%	NA
Japonica Intermediate	241	94.60%	5.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	57.80%	41.10%	1.11%	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
vg0610114031	C -> T	LOC_Os06g17430-LOC_Os06g17440	intergenic_region ; MODIFIER	silent_mutation	Average:70.691; most accessible tissue: Zhenshan97 panicle, score: 88.35	N	N	N	N
vg0610114031	C -> DEL	N	N	silent_mutation	Average:70.691; most accessible tissue: Zhenshan97 panicle, score: 88.35	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610114031	1.15E-06	1.15E-06	mr1011	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
vg0610114031	NA	7.46E-08	mr1090	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
vg0610114031	NA	5.88E-06	mr1121	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
vg0610114031	2.88E-06	NA	mr1065_2	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
vg0610114031	4.34E-06	NA	mr1068_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
vg0610114031	6.93E-06	2.47E-08	mr1068_2	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
vg0610114031	8.23E-07	NA	mr1078_2	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
vg0610114031	1.53E-06	NA	mr1087_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
vg0610114031	1.90E-07	NA	mr1087_2	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
vg0610114031	2.50E-06	NA	mr1090_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 10 of 34 entries

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Search for Variation information by Variation ID:

Detailed information for vg0610114031:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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