RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0716573684:

Variant ID: vg0716573684 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16573684
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, T: 0.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

CGCTTGGAAGCACAAGATGAAGTTGCATTTAATCTCGTTGCATCCAAGTATTTGGAAAGTTGTTTGTACAGGTATTGATGTACCCCATGATGACATGGAG[C/T]
TCACCTCGGAGCAAGAGCAACTCATCCACTGCAATGCTCAAGCTTCCAATGCAATTCTCTCTGCCTTGAGTCTGGAGGAGTTCAACAAGGTTGATGGACT

Reverse complement sequence

AGTCCATCAACCTTGTTGAACTCCTCCAGACTCAAGGCAGAGAGAATTGCATTGGAAGCTTGAGCATTGCAGTGGATGAGTTGCTCTTGCTCCGAGGTGA[G/A]
CTCCATGTCATCATGGGGTACATCAATACCTGTACAAACAACTTTCCAAATACTTGGATGCAACGAGATTAAATGCAACTTCATCTTGTGCTTCCAAGCG

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	89.70%	8.30%	0.28%	1.71%	NA
All Indica	2759	82.60%	14.00%	0.47%	2.94%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	71.80%	24.50%	0.67%	3.03%	NA
Indica II	465	97.60%	2.20%	0.00%	0.22%	NA
Indica III	913	82.70%	12.60%	0.33%	4.38%	NA
Indica Intermediate	786	81.90%	14.50%	0.76%	2.80%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg0716573684	C -> DEL	LOC_Os07g28370.1	N	frameshift_variant	Average:41.299; most accessible tissue: Zhenshan97 flag leaf, score: 61.926	N	N	N	N
vg0716573684	C -> T	LOC_Os07g28370.1	missense_variant ; p.Leu94Phe; MODERATE	nonsynonymous_codon ; L94F	Average:41.299; most accessible tissue: Zhenshan97 flag leaf, score: 61.926	probably damaging	2.145	TOLERATED	0.10

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
vg0716573684	NA	3.05E-06	mr1970	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
vg0716573684	NA	3.76E-07	mr1648_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
vg0716573684	NA	3.70E-08	mr1648_2	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
vg0716573684	NA	1.68E-06	mr1655_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
vg0716573684	NA	3.29E-06	mr1669_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
vg0716573684	NA	1.12E-07	mr1970_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

Showing 1 to 6 of 6 entries

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Search for Variation information by Variation ID:

Detailed information for vg0716573684:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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