RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0327037726:

Variant ID: vg0327037726 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 27037726
Reference Allele: C	Alternative Allele: T,G
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGTCCTGCACGACTCCAAGGCAGCTGCTGCAGACGCCATCAAGCACCATCAAGTTGCTGCGGAGAAGGAGTGCGGCCGCAAGCTTCGGGTGCTACGCAC[C/T,G]
AACAACGGTGGCGAGTTCACGGCGGCTGAGTTCGCGGCGTACTGCGCCGACGAGGGGATCCAGCGCCACTTCTCCGCGCCATACACCCCGCAGCAGAACG

Reverse complement sequence

CGTTCTGCTGCGGGGTGTATGGCGCGGAGAAGTGGCGCTGGATCCCCTCGTCGGCGCAGTACGCCGCGAACTCAGCCGCCGTGAACTCGCCACCGTTGTT[G/A,C]
GTGCGTAGCACCCGAAGCTTGCGGCCGCACTCCTTCTCCGCAGCAACTTGATGGTGCTTGATGGCGTCTGCAGCAGCTGCCTTGGAGTCGTGCAGGACCA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.40%	36.10%	0.53%	0.00%	G: 0.02%
All Indica	2759	97.60%	2.20%	0.25%	0.00%	NA
All Japonica	1512	1.20%	98.70%	0.07%	0.00%	G: 0.07%
Aus	269	84.80%	10.00%	5.20%	0.00%	NA
Indica I	595	98.70%	0.80%	0.50%	0.00%	NA
Indica II	465	98.10%	1.70%	0.22%	0.00%	NA
Indica III	913	97.40%	2.60%	0.00%	0.00%	NA
Indica Intermediate	786	96.70%	2.90%	0.38%	0.00%	NA
Temperate Japonica	767	0.40%	99.50%	0.00%	0.00%	G: 0.13%
Tropical Japonica	504	1.80%	98.00%	0.20%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	85.40%	1.04%	0.00%	NA
Intermediate	90	48.90%	48.90%	2.22%	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
vg0327037726	C -> T	LOC_Os03g47693-LOC_Os03g47720	intergenic_region ; MODIFIER	silent_mutation	Average:48.592; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0327037726	C -> G	LOC_Os03g47693-LOC_Os03g47720	intergenic_region ; MODIFIER	silent_mutation	Average:48.592; most accessible tissue: Minghui63 panicle, score: 66.554	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
vg0327037726	NA	9.51E-19	Yield	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0327037726	2.81E-06	NA	mr1114	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
vg0327037726	4.80E-06	NA	mr1116	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
vg0327037726	4.34E-08	NA	mr1117	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
vg0327037726	2.97E-08	NA	mr1118	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
vg0327037726	6.67E-07	NA	mr1119	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
vg0327037726	9.65E-09	NA	mr1123	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
vg0327037726	9.14E-09	NA	mr1240	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
vg0327037726	1.03E-08	NA	mr1242	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
vg0327037726	4.78E-06	NA	mr1247	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 48 entries

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Search for Variation information by Variation ID:

Detailed information for vg0327037726:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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