RiceVarMap2

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Detailed information for vg0209217731:

Variant ID: vg0209217731 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9217731
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTAATTATTCTGTACAATAATTAATAGAAACATAGTGAAAAAACCAAACCTAGATCTTCATCTTGCTGAACTCTTTTTGTCCATTGTGCAAGTTTCTTC[C/T]
GGTTCATTCGCATTTTCCTTGGTTGGCTACCCCTAGGATCCACAAAATCAAGGCCGGAAATCTGTCTCACAAATTTCGTGACCAAACCTGAAAACCCTTC

Reverse complement sequence

GAAGGGTTTTCAGGTTTGGTCACGAAATTTGTGAGACAGATTTCCGGCCTTGATTTTGTGGATCCTAGGGGTAGCCAACCAAGGAAAATGCGAATGAACC[G/A]
GAAGAAACTTGCACAATGGACAAAAAGAGTTCAGCAAGATGAAGATCTAGGTTTGGTTTTTTCACTATGTTTCTATTAATTATTGTACAGAATAATTAAT

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	45.70%	34.00%	13.80%	6.45%	NA
All Indica	2759	18.30%	57.00%	20.33%	4.42%	NA
All Japonica	1512	97.90%	0.80%	0.53%	0.73%	NA
Aus	269	12.30%	4.50%	24.16%	59.11%	NA
Indica I	595	43.50%	21.80%	30.76%	3.87%	NA
Indica II	465	14.80%	77.20%	3.23%	4.73%	NA
Indica III	913	2.50%	71.40%	23.33%	2.74%	NA
Indica Intermediate	786	19.50%	54.80%	19.08%	6.62%	NA
Temperate Japonica	767	98.30%	0.70%	0.26%	0.78%	NA
Tropical Japonica	504	97.20%	1.00%	0.79%	0.99%	NA
Japonica Intermediate	241	98.30%	0.80%	0.83%	0.00%	NA
VI/Aromatic	96	87.50%	0.00%	8.33%	4.17%	NA
Intermediate	90	64.40%	14.40%	11.11%	10.00%	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
vg0209217731	C -> T	LOC_Os02g16220.1	missense_variant ; p.Arg503Gln; MODERATE	nonsynonymous_codon ; R503Q	Average:14.749; most accessible tissue: Minghui63 flag leaf, score: 28.142	benign	0.383	TOLERATED	0.53
vg0209217731	C -> DEL	LOC_Os02g16220.1	N	frameshift_variant	Average:14.749; most accessible tissue: Minghui63 flag leaf, score: 28.142	N	N	N	N

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
vg0209217731	NA	8.96E-11	mr1281	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
vg0209217731	NA	2.44E-16	mr1040_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
vg0209217731	4.76E-06	NA	mr1167_2	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
vg0209217731	NA	3.42E-20	mr1362_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

Showing 1 to 4 of 4 entries

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Search for Variation information by Variation ID:

Detailed information for vg0209217731:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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