RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1013082033:

Variant ID: vg1013082033 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13082033
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CATTACCTTGGAATAATAGTTAAATTTATCTACCCATCTAATCGAACGTGCATGTGGTTACTTCATTGCGTGCATGAATGCTGTTCCTGGTATATATTGC[G/A]
TTGACACTTAGATACACAGGTACACAGGTCTTAAAAAAAGAGCACATAGGAACCAACTAACCTGGTGCGTCTAGGCCGCCTCAACTAAATGTGTTCCATA

Reverse complement sequence

TATGGAACACATTTAGTTGAGGCGGCCTAGACGCACCAGGTTAGTTGGTTCCTATGTGCTCTTTTTTTAAGACCTGTGTACCTGTGTATCTAAGTGTCAA[C/T]
GCAATATATACCAGGAACAGCATTCATGCACGCAATGAAGTAACCACATGCACGTTCGATTAGATGGGTAGATAAATTTAACTATTATTCCAAGGTAATG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.10%	11.70%	0.17%	0.00%	NA
All Indica	2759	80.90%	18.80%	0.25%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	92.20%	7.40%	0.37%	0.00%	NA
Indica I	595	80.80%	19.00%	0.17%	0.00%	NA
Indica II	465	92.90%	6.50%	0.65%	0.00%	NA
Indica III	913	78.00%	21.90%	0.11%	0.00%	NA
Indica Intermediate	786	77.20%	22.50%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	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	93.30%	6.70%	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
vg1013082033	G -> A	LOC_Os10g25300.1	intron_variant ; MODIFIER	silent_mutation	Average:68.195; most accessible tissue: Minghui63 flower, score: 81.835	N	N	N	N
vg1013082033	G -> A	LOC_Os10g25300.2	intron_variant ; MODIFIER	silent_mutation	Average:68.195; most accessible tissue: Minghui63 flower, score: 81.835	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013082033	NA	4.60E-09	mr1533	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
vg1013082033	NA	6.70E-09	mr1980	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
vg1013082033	4.50E-06	1.73E-13	mr1533_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
vg1013082033	NA	3.34E-09	mr1980_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 4 of 4 entries

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Search for Variation information by Variation ID:

Detailed information for vg1013082033:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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