Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1012431468:

Variant ID: vg1012431468 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12431468
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTATTATATCGATAATATTTACATTATTACAAAGGCACTTCAGGCCTGACAACAAAAAATAAACAGCAGCGGACTAGCGGGCCTACGGCTCCATCTTCA[C/T]
AGGCGCTCAACTAGGGTATAAGCCAGGACTCCACCTAAGACTTCTTCTCCAAAGCTTCTCTTACTAAAGGGGGGAGAGATAGAGCAAGAATGAGTATAAC

Reverse complement sequence

GTTATACTCATTCTTGCTCTATCTCTCCCCCCTTTAGTAAGAGAAGCTTTGGAGAAGAAGTCTTAGGTGGAGTCCTGGCTTATACCCTAGTTGAGCGCCT[G/A]
TGAAGATGGAGCCGTAGGCCCGCTAGTCCGCTGCTGTTTATTTTTTGTTGTCAGGCCTGAAGTGCCTTTGTAATAATGTAAATATTATCGATATAATAAA

Allele Frequencies:

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	91.30%	8.70%	0.02%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.04%	0.00%	NA
All Japonica	1512	97.40%	2.60%	0.00%	0.00%	NA
Aus	269	12.30%	87.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	98.70%	1.30%	0.00%	0.00%	NA
Indica Intermediate	786	97.60%	2.30%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	94.20%	5.80%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	15.60%	84.40%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012431468	C -> T	LOC_Os10g24260.1	upstream_gene_variant ; 2351.0bp to feature; MODIFIER	silent_mutation	Average:25.76; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N
vg1012431468	C -> T	LOC_Os10g24270.1	downstream_gene_variant ; 3704.0bp to feature; MODIFIER	silent_mutation	Average:25.76; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N
vg1012431468	C -> T	LOC_Os10g24250-LOC_Os10g24260	intergenic_region ; MODIFIER	silent_mutation	Average:25.76; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012431468	3.43E-06	NA	mr1448	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
vg1012431468	NA	7.79E-06	mr1522_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