RiceVarMap2

Detailed information for vg0213361533:

Variant ID: vg0213361533 (JBrowse)

Variation Type: SNP

Chromosome: chr02

Position: 13361533

Reference Allele: A

Alternative Allele: C

Primary Allele: C

Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, C: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTATATTTTCCTTGACCACAATATTAATCTAAAGTGGTCATATTGCTAAACTATGCACACACCTGCAGTTGAAGTGGCAGCCACGAAAGGATCTACCA[A/C]
TCTTAAAATCTGGAGACCAATATCTTTCATGGAATTCCCTCAAGGAAAGGGTTCCACTATTAGACTGGAAAAAGGGAAACATATCAAATCATGAAAAAGG

Reverse complement sequence

CCTTTTTCATGATTTGATATGTTTCCCTTTTTCCAGTCTAATAGTGGAACCCTTTCCTTGAGGGAATTCCATGAAAGATATTGGTCTCCAGATTTTAAGA[T/G]
TGGTAGATCCTTTCGTGGCTGCCACTTCAACTGCAGGTGTGTGCATAGTTTAGCAATATGACCACTTTAGATTAATATTGTGGTCAAGGAAAATATAGAG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.10%	37.80%	0.11%	0.00%	NA
All Indica	2759	96.70%	3.20%	0.11%	0.00%	NA
All Japonica	1512	1.60%	98.40%	0.00%	0.00%	NA
Aus	269	74.30%	25.30%	0.37%	0.00%	NA
Indica I	595	99.30%	0.50%	0.17%	0.00%	NA
Indica II	465	96.10%	3.70%	0.22%	0.00%	NA
Indica III	913	97.30%	2.70%	0.00%	0.00%	NA
Indica Intermediate	786	94.50%	5.30%	0.13%	0.00%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	2.40%	97.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	43.30%	55.60%	1.11%	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
vg0213361533	A -> C	LOC_Os02g22374.1	missense_variant ; p.Ile34Ser; MODERATE	nonsynonymous_codon ; I34S	Average:56.165; most accessible tissue: Zhenshan97 flower, score: 81.593	unknown	unknown	DELETERIOUS	0.00
vg0213361533	A -> C	LOC_Os02g22374.4	missense_variant ; p.Ile28Ser; MODERATE	nonsynonymous_codon ; I28S	Average:56.165; most accessible tissue: Zhenshan97 flower, score: 81.593	unknown	unknown	DELETERIOUS	0.00

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0213361533	NA	9.40E-08	mr1506	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
vg0213361533	NA	5.83E-14	mr1938_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 2 of 2 entries

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Search for Variation information by Variation ID:

Detailed information for vg0213361533:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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