RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0514784805:

Variant ID: vg0514784805 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14784805
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.08, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCATATGATTAGGACATCTTCAGAATCATGCATACAAATGGCGTCCTCGTTGTAGTACAGTAGTTACTAATTAGTCCGTGTACTACAGAAGATTATTC[C/T]
AGTCTCTGGATTGTAAGGAAGGTAAACAAGAGTGTACGTGGGACACACAGATTAATCAACTGGTTCAGTATCTCACAGGACAGTCCGTTAACAATCAAAT

Reverse complement sequence

ATTTGATTGTTAACGGACTGTCCTGTGAGATACTGAACCAGTTGATTAATCTGTGTGTCCCACGTACACTCTTGTTTACCTTCCTTACAATCCAGAGACT[G/A]
GAATAATCTTCTGTAGTACACGGACTAATTAGTAACTACTGTACTACAACGAGGACGCCATTTGTATGCATGATTCTGAAGATGTCCTAATCATATGAAG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.30%	48.00%	0.19%	0.55%	NA
All Indica	2759	78.50%	20.70%	0.22%	0.65%	NA
All Japonica	1512	7.90%	91.90%	0.00%	0.20%	NA
Aus	269	39.40%	60.60%	0.00%	0.00%	NA
Indica I	595	74.10%	25.00%	0.34%	0.50%	NA
Indica II	465	71.40%	27.50%	0.00%	1.08%	NA
Indica III	913	83.70%	16.00%	0.11%	0.22%	NA
Indica Intermediate	786	79.90%	18.70%	0.38%	1.02%	NA
Temperate Japonica	767	2.90%	97.10%	0.00%	0.00%	NA
Tropical Japonica	504	17.70%	81.70%	0.00%	0.60%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	0.00%	99.00%	1.04%	0.00%	NA
Intermediate	90	37.80%	54.40%	2.22%	5.56%	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
vg0514784805	C -> T	LOC_Os05g25430.1	3_prime_UTR_variant ; 944.0bp to feature; MODIFIER	silent_mutation	Average:61.17; most accessible tissue: Callus, score: 86.269	N	N	N	N
vg0514784805	C -> T	LOC_Os05g25430.2	3_prime_UTR_variant ; 944.0bp to feature; MODIFIER	silent_mutation	Average:61.17; most accessible tissue: Callus, score: 86.269	N	N	N	N
vg0514784805	C -> T	LOC_Os05g25420.1	downstream_gene_variant ; 2696.0bp to feature; MODIFIER	silent_mutation	Average:61.17; most accessible tissue: Callus, score: 86.269	N	N	N	N
vg0514784805	C -> DEL	N	N	silent_mutation	Average:61.17; most accessible tissue: Callus, score: 86.269	N	N	N	N

Showing 1 to 4 of 4 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514784805	NA	3.02E-06	mr1790	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
vg0514784805	NA	4.67E-06	mr1320_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 2 of 2 entries

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Search for Variation information by Variation ID:

Detailed information for vg0514784805:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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