RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0508659205:

Variant ID: vg0508659205 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 8659205
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGATATGTAGCTCCAGCACTTTTTAATCCAAAAGTCATTACAACCTATTCATATAAGCCGATTGCACCAAGACATCTGAAAGCAGTCTTATGAATATC[C/T]
TCTTCTACCATAAAAATTTGATTATATCCAGCATTGCCATCGATAAAACTTATAATCTTGTGCCCTGAAGCAGCATCTACCAACTGATCGGCAATCGGCA

Reverse complement sequence

TGCCGATTGCCGATCAGTTGGTAGATGCTGCTTCAGGGCACAAGATTATAAGTTTTATCGATGGCAATGCTGGATATAATCAAATTTTTATGGTAGAAGA[G/A]
GATATTCATAAGACTGCTTTCAGATGTCTTGGTGCAATCGGCTTATATGAATAGGTTGTAATGACTTTTGGATTAAAAAGTGCTGGAGCTACATATCAAA

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	88.60%	6.90%	0.93%	3.49%	NA
All Indica	2759	87.60%	4.90%	1.56%	5.94%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	29.00%	70.60%	0.37%	0.00%	NA
Indica I	595	98.20%	0.00%	0.34%	1.51%	NA
Indica II	465	98.50%	0.20%	0.65%	0.65%	NA
Indica III	913	77.50%	10.40%	2.41%	9.64%	NA
Indica Intermediate	786	85.00%	4.80%	2.04%	8.14%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	0.00%	1.11%	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
vg0508659205	C -> T	LOC_Os05g15260.1	downstream_gene_variant ; 2936.0bp to feature; MODIFIER	silent_mutation	Average:30.184; most accessible tissue: Zhenshan97 young leaf, score: 50.0	N	N	N	N
vg0508659205	C -> T	LOC_Os05g15270.1	intron_variant ; MODIFIER	silent_mutation	Average:30.184; most accessible tissue: Zhenshan97 young leaf, score: 50.0	N	N	N	N
vg0508659205	C -> DEL	N	N	silent_mutation	Average:30.184; most accessible tissue: Zhenshan97 young leaf, score: 50.0	N	N	N	N

Showing 1 to 3 of 3 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0508659205	1.57E-06	1.10E-22	mr1244	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
vg0508659205	NA	1.98E-06	mr1262	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
vg0508659205	NA	1.67E-06	mr1286	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
vg0508659205	NA	1.75E-06	mr1777	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 vg0508659205:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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