RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0802219948:

Variant ID: vg0802219948 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2219948
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 363. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTTTCCATCAAAGGTGGTTTTCACTGGCACGAAATGAGCTGATTTCGTGAGTCGATCCACGATTACCCAGATGGAGTCGTACCCGTTAGGGGTTCTTG[G/C]
CAAACCGGTGATGAAATCCATTCCGATCTCTTCCCATTTCCACTCGGGAATCGGTAGGGGTTGCAGCAGACCAGCTGGCCTCTGATGCTCTGCCTTGACT

Reverse complement sequence

AGTCAAGGCAGAGCATCAGAGGCCAGCTGGTCTGCTGCAACCCCTACCGATTCCCGAGTGGAAATGGGAAGAGATCGGAATGGATTTCATCACCGGTTTG[C/G]
CAAGAACCCCTAACGGGTACGACTCCATCTGGGTAATCGTGGATCGACTCACGAAATCAGCTCATTTCGTGCCAGTGAAAACCACCTTTGATGGAAAGAA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.00%	5.50%	28.29%	4.23%	NA
All Indica	2759	44.00%	9.50%	41.28%	5.26%	NA
All Japonica	1512	98.70%	0.00%	1.06%	0.26%	NA
Aus	269	25.70%	0.00%	57.99%	16.36%	NA
Indica I	595	32.40%	6.60%	50.08%	10.92%	NA
Indica II	465	57.20%	8.40%	27.31%	7.10%	NA
Indica III	913	46.00%	12.60%	40.53%	0.88%	NA
Indica Intermediate	786	42.60%	8.70%	43.77%	4.96%	NA
Temperate Japonica	767	98.80%	0.00%	0.91%	0.26%	NA
Tropical Japonica	504	99.00%	0.00%	0.79%	0.20%	NA
Japonica Intermediate	241	97.50%	0.00%	2.07%	0.41%	NA
VI/Aromatic	96	92.70%	0.00%	6.25%	1.04%	NA
Intermediate	90	71.10%	0.00%	22.22%	6.67%	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
vg0802219948	G -> C	LOC_Os08g04510.1	missense_variant ; p.Pro1397Ala; MODERATE	nonsynonymous_codon ; P1397A	Average:9.219; most accessible tissue: Minghui63 young leaf, score: 20.156	benign	1.084	DELETERIOUS	0.01
vg0802219948	G -> DEL	LOC_Os08g04510.1	N	frameshift_variant	Average:9.219; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802219948	6.04E-06	NA	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
vg0802219948	2.68E-06	NA	mr1063	Ind_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
vg0802219948	2.64E-06	NA	mr1161	Ind_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
vg0802219948	6.39E-08	NA	mr1750	Ind_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 4 of 4 entries

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Search for Variation information by Variation ID:

Detailed information for vg0802219948:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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