RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0316049074:

Variant ID: vg0316049074 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16049074
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCTCCTATCTCTTCTCATCTCTCTCTATATTCTCTCTCAGAGGCGTGCTCACACGGGGAGGCATCGGTCGCGGCGGAGATGGCGAGGACGGCGGCCAG[C/T]
GGAGTGAAGCGGGGCAGCAGCGGCGGTGGACGAGCGCACGGCCGGCGGAGCGGCATCATCGGCCGAGCAGAGTGGCAGCAGTGGCGAGCGAGCGCGCGGC

Reverse complement sequence

GCCGCGCGCTCGCTCGCCACTGCTGCCACTCTGCTCGGCCGATGATGCCGCTCCGCCGGCCGTGCGCTCGTCCACCGCCGCTGCTGCCCCGCTTCACTCC[G/A]
CTGGCCGCCGTCCTCGCCATCTCCGCCGCGACCGATGCCTCCCCGTGTGAGCACGCCTCTGAGAGAGAATATAGAGAGAGATGAGAAGAGATAGGAGATA

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	89.20%	10.40%	0.42%	0.00%	NA
All Indica	2759	99.30%	0.70%	0.00%	0.00%	NA
All Japonica	1512	70.60%	28.20%	1.19%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.90%	1.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.80%	0.00%	0.00%	NA
Temperate Japonica	767	70.30%	27.80%	1.96%	0.00%	NA
Tropical Japonica	504	69.80%	29.80%	0.40%	0.00%	NA
Japonica Intermediate	241	73.40%	26.10%	0.41%	0.00%	NA
VI/Aromatic	96	61.50%	38.50%	0.00%	0.00%	NA
Intermediate	90	86.70%	11.10%	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
vg0316049074	C -> T	LOC_Os03g27940.1	missense_variant ; p.Arg43Trp; MODERATE	nonsynonymous_codon ; R43W	Average:75.717; most accessible tissue: Zhenshan97 young leaf, score: 86.542	unknown	unknown	DELETERIOUS	0.00

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316049074	6.02E-06	NA	mr1087_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
vg0316049074	NA	2.37E-06	mr1329_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
vg0316049074	NA	8.47E-07	mr1524_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
vg0316049074	8.40E-06	NA	mr1549_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
vg0316049074	2.09E-07	NA	mr1757_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
vg0316049074	NA	9.37E-06	mr1757_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
vg0316049074	3.40E-06	NA	mr1980_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

Showing 1 to 7 of 7 entries

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Search for Variation information by Variation ID:

Detailed information for vg0316049074:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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