RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0233906724:

Variant ID: vg0233906724 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 33906724
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGATTATTTCTGATATTAGAAGAGCCGGTGCTTGATTTTAAATCTTTGTGCGAAATTGGCAAAACTGGAGACTAGGGGCGGTCTGACCGGCGTTGCACGG[C/T]
CGGTCTGATCGGTGACCAGGGGCAGTCTGACCGGCCGTATGCTGCCGGTCTGACCGGCGACCCCGAGCGGTCTGACCGGCCCTGCGTGGCCGGTCTGACC

Reverse complement sequence

GGTCAGACCGGCCACGCAGGGCCGGTCAGACCGCTCGGGGTCGCCGGTCAGACCGGCAGCATACGGCCGGTCAGACTGCCCCTGGTCACCGATCAGACCG[G/A]
CCGTGCAACGCCGGTCAGACCGCCCCTAGTCTCCAGTTTTGCCAATTTCGCACAAAGATTTAAAATCAAGCACCGGCTCTTCTAATATCAGAAATAATCC

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	87.90%	1.90%	10.22%	0.00%	NA
All Indica	2759	79.60%	3.30%	17.07%	0.00%	NA
All Japonica	1512	99.70%	0.00%	0.33%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	86.10%	1.70%	12.27%	0.00%	NA
Indica II	465	73.50%	7.50%	18.92%	0.00%	NA
Indica III	913	72.80%	4.10%	23.11%	0.00%	NA
Indica Intermediate	786	86.30%	1.10%	12.60%	0.00%	NA
Temperate Japonica	767	99.60%	0.00%	0.39%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	95.60%	0.00%	4.44%	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
vg0233906724	C -> T	LOC_Os02g55360.1	upstream_gene_variant ; 2291.0bp to feature; MODIFIER	silent_mutation	Average:27.296; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0233906724	C -> T	LOC_Os02g55350.1	intron_variant ; MODIFIER	silent_mutation	Average:27.296; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	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
vg0233906724	NA	4.05E-10	mr1039	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
vg0233906724	5.38E-10	NA	mr1039_2	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
vg0233906724	8.72E-08	4.89E-12	mr1039_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
vg0233906724	7.76E-10	NA	mr1632_2	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
vg0233906724	2.20E-08	1.23E-11	mr1632_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

Showing 1 to 5 of 5 entries

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Search for Variation information by Variation ID:

Detailed information for vg0233906724:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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