RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0407826287:

Variant ID: vg0407826287 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7826287
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

AGGATAATATCTGATCGTGGTACCCAATTCACCTCCCATTTCTGGAATAAAGTACATGAAGCTCTGGGAAGTTACCTCGCCTTTAGCACGGCATATCATC[C/T]
GCAGACAGATGGACAGACTGAAAGAACAAATCAAGTGCTAGAAGATATGTGAAGGTCTTGTGCCTTGGATTTCACCAAGGATTGGGAAAGGTGCCTACCA

Reverse complement sequence

TGGTAGGCACCTTTCCCAATCCTTGGTGAAATCCAAGGCACAAGACCTTCACATATCTTCTAGCACTTGATTTGTTCTTTCAGTCTGTCCATCTGTCTGC[G/A]
GATGATATGCCGTGCTAAAGGCGAGGTAACTTCCCAGAGCTTCATGTACTTTATTCCAGAAATGGGAGGTGAATTGGGTACCACGATCAGATATTATCCT

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	64.80%	20.60%	1.33%	13.22%	NA
All Indica	2759	41.20%	35.00%	2.21%	21.57%	NA
All Japonica	1512	99.60%	0.20%	0.00%	0.20%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	10.60%	83.20%	1.34%	4.87%	NA
Indica II	465	53.50%	17.20%	1.94%	27.31%	NA
Indica III	913	52.40%	15.60%	2.74%	29.35%	NA
Indica Intermediate	786	44.30%	31.60%	2.42%	21.76%	NA
Temperate Japonica	767	99.70%	0.10%	0.00%	0.13%	NA
Tropical Japonica	504	99.40%	0.20%	0.00%	0.40%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	0.00%	0.00%	12.50%	NA
Intermediate	90	75.60%	7.80%	2.22%	14.44%	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
vg0407826287	C -> DEL	LOC_Os04g14010.1	N	frameshift_variant	Average:52.988; most accessible tissue: Callus, score: 80.449	N	N	N	N
vg0407826287	C -> T	LOC_Os04g14010.1	missense_variant ; p.Pro92Leu; MODERATE	nonsynonymous_codon ; P92L	Average:52.988; most accessible tissue: Callus, score: 80.449	possibly damaging	1.777	DELETERIOUS	0.02

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
vg0407826287	1.02E-06	5.86E-45	mr1026	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
vg0407826287	NA	1.02E-21	mr1026	Ind_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
vg0407826287	NA	2.38E-06	mr1113	Ind_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
vg0407826287	NA	4.44E-06	mr1114	Ind_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
vg0407826287	NA	1.73E-06	mr1116	Ind_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
vg0407826287	NA	8.83E-17	mr1118	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
vg0407826287	3.11E-06	6.56E-19	mr1118	Ind_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
vg0407826287	NA	7.86E-07	mr1120	Ind_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
vg0407826287	1.04E-06	1.10E-42	mr1161	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
vg0407826287	NA	1.32E-20	mr1161	Ind_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 34 entries

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Search for Variation information by Variation ID:

Detailed information for vg0407826287:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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