RiceVarMap2

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Detailed information for vg0400963078:

Variant ID: vg0400963078 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 963078
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

CCCCTCACCTACCTACTAATCAATATAACTTTTACATTTATTAAGGGTATTATGGTCTTTTATCTCTTTCCTTAATTTTTTCTTGGGATGCTAGGGTTTA[G/C]
TTTATTTGGGGACAGAGGGAGTACGTAATATGGAATAAGTTCATTTTGACTCTCTCAACAAGTGACCAAATCTGATTCGTATCTCTCAACCACAATACCA

Reverse complement sequence

TGGTATTGTGGTTGAGAGATACGAATCAGATTTGGTCACTTGTTGAGAGAGTCAAAATGAACTTATTCCATATTACGTACTCCCTCTGTCCCCAAATAAA[C/G]
TAAACCCTAGCATCCCAAGAAAAAATTAAGGAAAGAGATAAAAGACCATAATACCCTTAATAAATGTAAAAGTTATATTGATTAGTAGGTAGGTGAGGGG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.00%	1.60%	2.29%	0.06%	NA
All Indica	2759	99.20%	0.30%	0.51%	0.04%	NA
All Japonica	1512	89.60%	4.30%	5.95%	0.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.80%	0.30%	0.84%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	0.50%	1.02%	0.13%	NA
Temperate Japonica	767	98.40%	0.70%	0.91%	0.00%	NA
Tropical Japonica	504	79.80%	8.50%	11.31%	0.40%	NA
Japonica Intermediate	241	82.20%	7.10%	10.79%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	2.20%	4.44%	0.00%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

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Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400963078	G -> C	LOC_Os04g02560.1	upstream_gene_variant ; 3037.0bp to feature; MODIFIER	silent_mutation	Average:45.84; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0400963078	G -> C	LOC_Os04g02570.1	downstream_gene_variant ; 4065.0bp to feature; MODIFIER	silent_mutation	Average:45.84; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0400963078	G -> C	LOC_Os04g02580.1	downstream_gene_variant ; 4889.0bp to feature; MODIFIER	silent_mutation	Average:45.84; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0400963078	G -> C	LOC_Os04g02560-LOC_Os04g02570	intergenic_region ; MODIFIER	silent_mutation	Average:45.84; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0400963078	G -> DEL	N	N	silent_mutation	Average:45.84; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N

Showing 1 to 5 of 5 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400963078	3.25E-06	2.59E-07	mr1682	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

Showing 1 to 1 of 1 entries

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Search for Variation information by Variation ID:

Detailed information for vg0400963078:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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