RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0300244541:

Variant ID: vg0300244541 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 244541
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGAAAAGAAAAGAAAGAGGGAGGAGGGGTAGACTTTCCTCGGGCGGCTAGGGCGCGGCCCGAGAGGAGAGGCGCGGCTCGGCCGAGCTAATGGGCCGGC[T/C]
GACCCGAGAAGGCAGCCCAAGGGCACGCGCGGGGAGAGAGGGAGGGGGAACCGGTGGGCCGGGTCCACCTCACGTGGTCCCGAGTGGGACCCGCTTGTTG

Reverse complement sequence

CAACAAGCGGGTCCCACTCGGGACCACGTGAGGTGGACCCGGCCCACCGGTTCCCCCTCCCTCTCTCCCCGCGCGTGCCCTTGGGCTGCCTTCTCGGGTC[A/G]
GCCGGCCCATTAGCTCGGCCGAGCCGCGCCTCTCCTCTCGGGCCGCGCCCTAGCCGCCCGAGGAAAGTCTACCCCTCCTCCCTCTTTCTTTTCTTTTCAA

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	80.60%	18.80%	0.66%	0.00%	NA
All Indica	2759	97.50%	2.30%	0.18%	0.00%	NA
All Japonica	1512	45.60%	52.70%	1.65%	0.00%	NA
Aus	269	97.80%	1.90%	0.37%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	91.60%	8.00%	0.43%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	97.30%	2.30%	0.38%	0.00%	NA
Temperate Japonica	767	13.80%	84.60%	1.56%	0.00%	NA
Tropical Japonica	504	87.30%	11.70%	0.99%	0.00%	NA
Japonica Intermediate	241	59.80%	36.90%	3.32%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	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
vg0300244541	T -> C	LOC_Os03g01330-LOC_Os03g01340	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0300244541	NA	2.47E-11	Plant_height	Jap_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
vg0300244541	NA	6.50E-30	mr1137	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
vg0300244541	NA	8.69E-11	mr1137	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
vg0300244541	NA	1.04E-06	mr1180	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
vg0300244541	NA	2.79E-10	mr1183	Jap_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
vg0300244541	NA	4.05E-09	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
vg0300244541	NA	3.68E-07	mr1530	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
vg0300244541	NA	7.99E-06	mr1530	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
vg0300244541	9.16E-06	7.14E-27	mr1617	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
vg0300244541	NA	2.55E-09	mr1617	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 10 of 16 entries

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Search for Variation information by Variation ID:

Detailed information for vg0300244541:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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