Search for Variation information by Variation ID:

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

Detailed information for vg1013638393:

Variant ID: vg1013638393 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13638393
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTGGGCTTGGCTTAGTTTCTAATTTTTTTTTCCTAAAAATATAACATTAAATCTTTGGACATCCAAATAGAGCATTAAATATAGATACAATGAATAATT[G/A]
CACAGTTCGCACAAAAATCGTGAGACGAAACTTTTGAGCCTAATTAGTCTATGATTAGTTATAAGTGCTATAGTAACCATATGTGCTAATGATGGATTAA

Reverse complement sequence

TTAATCCATCATTAGCACATATGGTTACTATAGCACTTATAACTAATCATAGACTAATTAGGCTCAAAAGTTTCGTCTCACGATTTTTGTGCGAACTGTG[C/T]
AATTATTCATTGTATCTATATTTAATGCTCTATTTGGATGTCCAAAGATTTAATGTTATATTTTTAGGAAAAAAAAATTAGAAACTAAGCCAAGCCCAAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.10%	21.70%	0.21%	0.00%	NA
All Indica	2759	74.40%	25.30%	0.33%	0.00%	NA
All Japonica	1512	96.90%	3.10%	0.00%	0.00%	NA
Aus	269	8.20%	91.80%	0.00%	0.00%	NA
Indica I	595	69.60%	29.70%	0.67%	0.00%	NA
Indica II	465	96.60%	3.40%	0.00%	0.00%	NA
Indica III	913	68.90%	30.90%	0.22%	0.00%	NA
Indica Intermediate	786	71.20%	28.40%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	91.50%	8.50%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	81.10%	17.80%	1.11%	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
vg1013638393	G -> A	LOC_Os10g26300-LOC_Os10g26320	intergenic_region ; MODIFIER	silent_mutation	Average:75.946; most accessible tissue: Minghui63 panicle, score: 99.422	N	N	N	N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg1013638393	G	A	0.0	0.01	0.0	0.0	0.02	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013638393	2.63E-16	NA	mr1533	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
vg1013638393	4.17E-18	1.48E-23	mr1533	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
vg1013638393	5.47E-17	NA	mr1980	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
vg1013638393	2.62E-19	2.34E-24	mr1980	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
vg1013638393	8.84E-16	NA	mr1533_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
vg1013638393	3.08E-19	2.69E-29	mr1533_2	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
vg1013638393	3.61E-07	NA	mr1980_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
vg1013638393	5.04E-08	1.74E-12	mr1980_2	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