RiceVarMap2

Detailed information for vg0403275975:

Variant ID: vg0403275975 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 3275975

Reference Allele: A

Alternative Allele: G

Primary Allele: A

Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 30. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTTTTGAACCATGTCAGCTGCCACGTGGCAAGCCCTAGGATTTTGTGACAATAAATCAATGTCATATGCTTGTGACAATGAATGTTCAAACGTCAC[A/G]
TGATGAATTTATGACGGTGGCTTTTTGACGTTTGAAATTACGTCATCTGTTTGTCACAAATCTTAATTTTTGACATAATTTTCATATATTATGACATAAT

Reverse complement sequence

ATTATGTCATAATATATGAAAATTATGTCAAAAATTAAGATTTGTGACAAACAGATGACGTAATTTCAAACGTCAAAAAGCCACCGTCATAAATTCATCA[T/C]
GTGACGTTTGAACATTCATTGTCACAAGCATATGACATTGATTTATTGTCACAAAATCCTAGGGCTTGCCACGTGGCAGCTGACATGGTTCAAAAAAAAA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.20%	2.50%	8.04%	59.27%	NA
All Indica	2759	20.40%	4.00%	12.40%	63.18%	NA
All Japonica	1512	52.40%	0.30%	0.79%	46.56%	NA
Aus	269	12.30%	0.40%	5.20%	82.16%	NA
Indica I	595	37.00%	1.50%	2.18%	59.33%	NA
Indica II	465	17.40%	4.10%	21.72%	56.77%	NA
Indica III	913	11.20%	4.60%	11.72%	72.51%	NA
Indica Intermediate	786	20.50%	5.10%	15.39%	59.03%	NA
Temperate Japonica	767	83.60%	0.40%	0.91%	15.12%	NA
Tropical Japonica	504	15.30%	0.00%	0.40%	84.33%	NA
Japonica Intermediate	241	30.70%	0.40%	1.24%	67.63%	NA
VI/Aromatic	96	12.50%	0.00%	0.00%	87.50%	NA
Intermediate	90	30.00%	2.20%	13.33%	54.44%	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
vg0403275975	A -> DEL	N	N	silent_mutation	Average:19.52; most accessible tissue: Callus, score: 95.535	N	N	N	N
vg0403275975	A -> G	LOC_Os04g06280.1	intron_variant ; MODIFIER	silent_mutation	Average:19.52; most accessible tissue: Callus, score: 95.535	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
vg0403275975	NA	2.11E-08	mr1027_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
vg0403275975	NA	5.70E-09	mr1580_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
vg0403275975	4.94E-06	1.27E-10	mr1825_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

Showing 1 to 3 of 3 entries

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Search for Variation information by Variation ID:

Detailed information for vg0403275975:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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