RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0308388246:

Variant ID: vg0308388246 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 8388246
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGATTCATAGTAGAAATGCTTATATTTTGGAATGGAGGGAGTACCAAATAATGTGTTTTGTTACTATAAAAATTCTTTTTATAACAAAAGTAGCCATTTA[T/C]
CAGTCTTAAAAAAAACAAAATTAGCCTTATGCGCAACAAGTTAGATCTACCCCTAAAAAGGAACTTGTTTTTGGTTCCGTGAGTCTCATCGGTTGCCCAT

Reverse complement sequence

ATGGGCAACCGATGAGACTCACGGAACCAAAAACAAGTTCCTTTTTAGGGGTAGATCTAACTTGTTGCGCATAAGGCTAATTTTGTTTTTTTTAAGACTG[A/G]
TAAATGGCTACTTTTGTTATAAAAAGAATTTTTATAGTAACAAAACACATTATTTGGTACTCCCTCCATTCCAAAATATAAGCATTTCTACTATGAATCT

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	84.30%	15.70%	0.06%	0.00%	NA
All Indica	2759	97.90%	2.00%	0.04%	0.00%	NA
All Japonica	1512	78.30%	21.60%	0.13%	0.00%	NA
Aus	269	4.10%	95.90%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.20%	1.80%	0.00%	0.00%	NA
Indica Intermediate	786	95.20%	4.80%	0.00%	0.00%	NA
Temperate Japonica	767	59.50%	40.40%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	92.90%	6.60%	0.41%	0.00%	NA
VI/Aromatic	96	16.70%	83.30%	0.00%	0.00%	NA
Intermediate	90	76.70%	23.30%	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
vg0308388246	T -> C	LOC_Os03g15330.1	upstream_gene_variant ; 1191.0bp to feature; MODIFIER	silent_mutation	Average:36.427; most accessible tissue: Callus, score: 80.931	N	N	N	N
vg0308388246	T -> C	LOC_Os03g15320.1	downstream_gene_variant ; 2155.0bp to feature; MODIFIER	silent_mutation	Average:36.427; most accessible tissue: Callus, score: 80.931	N	N	N	N
vg0308388246	T -> C	LOC_Os03g15330-LOC_Os03g15340	intergenic_region ; MODIFIER	silent_mutation	Average:36.427; most accessible tissue: Callus, score: 80.931	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
vg0308388246	NA	8.32E-06	mr1026	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
vg0308388246	NA	2.38E-09	mr1157	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
vg0308388246	NA	4.70E-06	mr1171	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
vg0308388246	NA	1.22E-06	mr1171	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
vg0308388246	NA	1.36E-14	mr1231	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
vg0308388246	NA	7.58E-22	mr1244	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
vg0308388246	NA	8.47E-07	mr1321	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
vg0308388246	NA	5.24E-11	mr1328	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
vg0308388246	NA	1.83E-06	mr1328	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
vg0308388246	NA	2.79E-14	mr1403	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 33 entries

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Search for Variation information by Variation ID:

Detailed information for vg0308388246:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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