RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0134236950:

Variant ID: vg0134236950 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 34236950
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TTGAACCCGGTCTAACCGTCCAAACTCCGCAGTCTAACCAGTCCGTCGGTCTGACCACCCTGCCGGCCCAGTTTAACCGTCATACATGCACACCTCACGC[G/A]
CCTTCTCCGGAGCCGTATACTCACCGCATCACCTTGATCACCACAAAGCTGCACCATGCCTCTCGTCTTGTGCCCGTGAGCCACGCCGCCAAAACAACGT

Reverse complement sequence

ACGTTGTTTTGGCGGCGTGGCTCACGGGCACAAGACGAGAGGCATGGTGCAGCTTTGTGGTGATCAAGGTGATGCGGTGAGTATACGGCTCCGGAGAAGG[C/T]
GCGTGAGGTGTGCATGTATGACGGTTAAACTGGGCCGGCAGGGTGGTCAGACCGACGGACTGGTTAGACTGCGGAGTTTGGACGGTTAGACCGGGTTCAA

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	78.20%	21.00%	0.00%	0.76%	NA
All Indica	2759	98.00%	2.00%	0.00%	0.00%	NA
All Japonica	1512	37.20%	60.40%	0.00%	2.38%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.50%	3.50%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	96.10%	3.90%	0.00%	0.00%	NA
Temperate Japonica	767	8.70%	87.00%	0.00%	4.30%	NA
Tropical Japonica	504	68.10%	31.70%	0.00%	0.20%	NA
Japonica Intermediate	241	63.10%	36.10%	0.00%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	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
vg0134236950	G -> A	LOC_Os01g59230.1	intron_variant ; MODIFIER	silent_mutation	Average:66.053; most accessible tissue: Zhenshan97 flower, score: 80.159	N	N	N	N
vg0134236950	G -> DEL	N	N	silent_mutation	Average:66.053; most accessible tissue: Zhenshan97 flower, score: 80.159	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0134236950	NA	1.29E-12	mr1010	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
vg0134236950	NA	5.77E-06	mr1503	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
vg0134236950	8.12E-06	NA	mr1679	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
vg0134236950	2.62E-06	NA	mr1691	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
vg0134236950	NA	1.48E-07	mr1180_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 5 of 5 entries

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Search for Variation information by Variation ID:

Detailed information for vg0134236950:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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