RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0726583506:

Variant ID: vg0726583506 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 26583506
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

ATGAAAGAAAGAATGTACAAGATCTTCTCAAACGCTATTGTTGTCAGCTATTCACACCTGCTACCCGTTGTGCCATTCAATGCATTCAATCCTCCTCCAC[C/T]
GGTACGTATTCATACACTTCAACCTTTCTCAAAATATGGTCTTGCTTTCTTGTTGAATCAGTTAACAATGAAGGATATTACACCCAGGAATTTGCTTTGA

Reverse complement sequence

TCAAAGCAAATTCCTGGGTGTAATATCCTTCATTGTTAACTGATTCAACAAGAAAGCAAGACCATATTTTGAGAAAGGTTGAAGTGTATGAATACGTACC[G/A]
GTGGAGGAGGATTGAATGCATTGAATGGCACAACGGGTAGCAGGTGTGAATAGCTGACAACAATAGCGTTTGAGAAGATCTTGTACATTCTTTCTTTCAT

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	94.70%	1.80%	0.72%	2.79%	NA
All Indica	2759	97.40%	0.10%	0.51%	2.03%	NA
All Japonica	1512	94.20%	5.20%	0.46%	0.20%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	94.10%	0.00%	0.77%	5.15%	NA
Indica Intermediate	786	98.10%	0.10%	0.76%	1.02%	NA
Temperate Japonica	767	88.90%	10.20%	0.91%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	27.10%	0.00%	12.50%	60.42%	NA
Intermediate	90	82.20%	2.20%	1.11%	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
vg0726583506	C -> DEL	LOC_Os07g44520.1	N	frameshift_variant	Average:23.873; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N
vg0726583506	C -> T	LOC_Os07g44520.1	missense_variant&splice_region_variant ; p.Pro295Leu; MODERATE	nonsynonymous_codon ; P295L	Average:23.873; most accessible tissue: Minghui63 root, score: 36.81	unknown	unknown	DELETERIOUS	0.00

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
vg0726583506	NA	3.44E-07	mr1062	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
vg0726583506	7.43E-06	7.43E-06	mr1284	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
vg0726583506	3.21E-07	1.68E-09	mr1358	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
vg0726583506	6.35E-06	6.35E-06	mr1476	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
vg0726583506	NA	2.70E-07	mr1585	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
vg0726583506	4.05E-06	4.05E-06	mr1849	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
vg0726583506	NA	1.74E-06	mr1585_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

Showing 1 to 7 of 7 entries

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Search for Variation information by Variation ID:

Detailed information for vg0726583506:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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