RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1124320687:

Variant ID: vg1124320687 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24320687
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

CCACACACTAGCTTTGCAATTAGAGAAGCCATGATGAGGTGTTTAATTGAGTGGGGCTTGAGTAGCAAACTGTTCACCTTAGACAATGCTATTAACAACA[C/T]
ACTGTTTGTCAAGAATTAGTGAAAAATCTCAAGGATGAGTTGGTATTGGAAGGTACTTCCTCCGTCCCACAATACTTGTCTACTAGCATTCAAAAATTGT

Reverse complement sequence

ACAATTTTTGAATGCTAGTAGACAAGTATTGTGGGACGGAGGAAGTACCTTCCAATACCAACTCATCCTTGAGATTTTTCACTAATTCTTGACAAACAGT[G/A]
TGTTGTTAATAGCATTGTCTAAGGTGAACAGTTTGCTACTCAAGCCCCACTCAATTAAACACCTCATCATGGCTTCTCTAATTGCAAAGCTAGTGTGTGG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.70%	7.70%	0.11%	1.54%	NA
All Indica	2759	99.00%	0.40%	0.00%	0.58%	NA
All Japonica	1512	77.40%	22.50%	0.07%	0.00%	NA
Aus	269	77.00%	0.40%	1.49%	21.19%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.80%	1.90%	0.00%	0.22%	NA
Indica III	913	99.20%	0.00%	0.00%	0.77%	NA
Indica Intermediate	786	98.70%	0.30%	0.00%	1.02%	NA
Temperate Japonica	767	92.70%	7.20%	0.13%	0.00%	NA
Tropical Japonica	504	52.80%	47.20%	0.00%	0.00%	NA
Japonica Intermediate	241	80.50%	19.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg1124320687	C -> T	LOC_Os11g40700.1	downstream_gene_variant ; 3195.0bp to feature; MODIFIER	silent_mutation	Average:37.416; most accessible tissue: Callus, score: 69.183	N	N	N	N
vg1124320687	C -> T	LOC_Os11g40690-LOC_Os11g40700	intergenic_region ; MODIFIER	silent_mutation	Average:37.416; most accessible tissue: Callus, score: 69.183	N	N	N	N
vg1124320687	C -> DEL	N	N	silent_mutation	Average:37.416; most accessible tissue: Callus, score: 69.183	N	N	N	N

Showing 1 to 3 of 3 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124320687	2.67E-06	NA	mr1238	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
vg1124320687	NA	4.37E-07	mr1248	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
vg1124320687	NA	4.95E-07	mr1554	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
vg1124320687	8.29E-06	7.25E-13	mr1900	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
vg1124320687	NA	7.00E-06	mr1900	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
vg1124320687	2.41E-10	NA	mr1238_2	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
vg1124320687	1.16E-06	NA	mr1238_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
vg1124320687	NA	5.20E-09	mr1354_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
vg1124320687	2.23E-10	NA	mr1484_2	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
vg1124320687	NA	2.34E-07	mr1554_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 10 of 16 entries

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Search for Variation information by Variation ID:

Detailed information for vg1124320687:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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