RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0105166793:

Variant ID: vg0105166793 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5166793
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAGGCGAGACGGCGGCGGCGGAAGCCGGCGACGAGACGAAGCGAGAGGACCTAGTAGAGATCGAGGTGACGACGACGAGCGGCGGCAGCGGAGCGGCGG[C/A]
TGCGGCGGCGACAGGAGGAGATCAAGAGACTTGTTGCACGCTCAACGTGGACTTGCGCGGCGGCGGCGGCGGAGGCATGAGCACGACGGACGTTGTGCTC

Reverse complement sequence

GAGCACAACGTCCGTCGTGCTCATGCCTCCGCCGCCGCCGCCGCGCAAGTCCACGTTGAGCGTGCAACAAGTCTCTTGATCTCCTCCTGTCGCCGCCGCA[G/T]
CCGCCGCTCCGCTGCCGCCGCTCGTCGTCGTCACCTCGATCTCTACTAGGTCCTCTCGCTTCGTCTCGTCGCCGGCTTCCGCCGCCGCCGTCTCGCCTTT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.40%	27.40%	0.15%	0.00%	NA
All Indica	2759	99.00%	0.90%	0.04%	0.00%	NA
All Japonica	1512	23.60%	76.30%	0.13%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	98.60%	1.30%	0.13%	0.00%	NA
Temperate Japonica	767	15.90%	84.00%	0.13%	0.00%	NA
Tropical Japonica	504	37.50%	62.30%	0.20%	0.00%	NA
Japonica Intermediate	241	19.10%	80.90%	0.00%	0.00%	NA
VI/Aromatic	96	19.80%	79.20%	1.04%	0.00%	NA
Intermediate	90	54.40%	42.20%	3.33%	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
vg0105166793	C -> A	LOC_Os01g09930.1	missense_variant ; p.Ala290Asp; MODERATE	nonsynonymous_codon ; A290D	Average:63.111; most accessible tissue: Zhenshan97 root, score: 82.361	unknown	unknown	TOLERATED	0.58

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
vg0105166793	2.31E-22	5.02E-07	mr1057	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
vg0105166793	1.73E-14	5.94E-19	mr1057	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
vg0105166793	1.33E-06	8.69E-30	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
vg0105166793	8.07E-06	1.77E-31	mr1309	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
vg0105166793	NA	4.28E-18	mr1484	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
vg0105166793	NA	1.50E-07	mr1677	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
vg0105166793	NA	8.49E-06	mr1677	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
vg0105166793	NA	8.38E-26	mr1841	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
vg0105166793	1.42E-06	1.64E-17	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
vg0105166793	NA	1.06E-11	mr1945	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 18 entries

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Search for Variation information by Variation ID:

Detailed information for vg0105166793:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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