RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0211188937:

Variant ID: vg0211188937 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 11188937
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGATGACAAAGTAATTTACATTTAATTTATAACCATAGTATAAATGCTTTGCAATGTAATACCTGGTGGCAGTGACATGATTTTGCAGTGTCCTAGAT[A/T]
AAAGTCACGAAACTAGAGTGCTCGGTTGCAATTTTTTTTGGCCTAAAAGTATCTATGTACGAGGATCCTGAGACATTTTGATTTAATGACTAACTAAAAG

Reverse complement sequence

CTTTTAGTTAGTCATTAAATCAAAATGTCTCAGGATCCTCGTACATAGATACTTTTAGGCCAAAAAAAATTGCAACCGAGCACTCTAGTTTCGTGACTTT[T/A]
ATCTAGGACACTGCAAAATCATGTCACTGCCACCAGGTATTACATTGCAAAGCATTTATACTATGGTTATAAATTAAATGTAAATTACTTTGTCATCGAA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.10%	9.50%	0.36%	0.00%	NA
All Indica	2759	99.40%	0.60%	0.00%	0.00%	NA
All Japonica	1512	75.90%	23.10%	0.99%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	1.00%	0.00%	0.00%	NA
Temperate Japonica	767	92.20%	6.60%	1.17%	0.00%	NA
Tropical Japonica	504	53.20%	46.20%	0.60%	0.00%	NA
Japonica Intermediate	241	71.40%	27.40%	1.24%	0.00%	NA
VI/Aromatic	96	29.20%	70.80%	0.00%	0.00%	NA
Intermediate	90	82.20%	15.60%	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
vg0211188937	A -> T	LOC_Os02g19180.1	upstream_gene_variant ; 4548.0bp to feature; MODIFIER	silent_mutation	Average:60.248; most accessible tissue: Callus, score: 82.577	N	N	N	N
vg0211188937	A -> T	LOC_Os02g19200.1	intron_variant ; MODIFIER	silent_mutation	Average:60.248; most accessible tissue: Callus, score: 82.577	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0211188937	NA	2.52E-06	mr1835	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
vg0211188937	7.72E-07	NA	mr1008_2	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
vg0211188937	3.80E-06	3.12E-10	mr1039_2	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
vg0211188937	7.27E-08	NA	mr1042_2	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
vg0211188937	4.79E-06	NA	mr1042_2	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
vg0211188937	NA	9.66E-07	mr1057_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
vg0211188937	NA	8.80E-11	mr1398_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
vg0211188937	NA	4.52E-07	mr1401_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
vg0211188937	NA	2.53E-09	mr1510_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
vg0211188937	NA	6.38E-07	mr1510_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

Showing 1 to 10 of 33 entries

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Search for Variation information by Variation ID:

Detailed information for vg0211188937:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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