Search for Variation information by Variation ID:

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

Detailed information for vg0130874710:

Variant ID: vg0130874710 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 30874710
Reference Allele: T	Alternative Allele: C,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.10, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

ATTAAAGACAGCGCTAGATCCCTACAGCTGGCCTCTGTAGGTACCGGATAGGGTCAGTCCAGGCATATCTCTGATGTCGATATCCGGCGGCGTGTCTTGG[T/C,A]
GTATGTTGGCTTGTATGTTGTGGCTTTTGTTGTTCTGTGTATGTTGATTGTGTCTCCTCTCCTCCTAGGGGGCCTTGTATTTATACCCATAGGTGTCCCC

Reverse complement sequence

GGGGACACCTATGGGTATAAATACAAGGCCCCCTAGGAGGAGAGGAGACACAATCAACATACACAGAACAACAAAAGCCACAACATACAAGCCAACATAC[A/G,T]
CCAAGACACGCCGCCGGATATCGACATCAGAGATATGCCTGGACTGACCCTATCCGGTACCTACAGAGGCCAGCTGTAGGGATCTAGCGCTGTCTTTAAT

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	63.10%	32.90%	1.38%	2.20%	A: 0.40%
All Indica	2759	98.00%	2.00%	0.00%	0.07%	NA
All Japonica	1512	1.10%	91.40%	1.79%	5.16%	A: 0.60%
Aus	269	82.90%	16.70%	0.00%	0.37%	NA
Indica I	595	97.00%	3.00%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	99.70%	0.20%	0.00%	0.11%	NA
Indica Intermediate	786	96.20%	3.70%	0.00%	0.13%	NA
Temperate Japonica	767	0.40%	95.00%	2.22%	2.09%	A: 0.26%
Tropical Japonica	504	1.40%	89.10%	0.79%	7.74%	A: 0.99%
Japonica Intermediate	241	2.50%	84.60%	2.49%	9.54%	A: 0.83%
VI/Aromatic	96	11.50%	30.20%	32.29%	15.62%	A: 10.42%
Intermediate	90	31.10%	52.20%	7.78%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0130874710	T -> A	LOC_Os01g53720.2	upstream_gene_variant ; 4290.0bp to feature; MODIFIER	silent_mutation	Average:72.642; most accessible tissue: Zhenshan97 flag leaf, score: 85.998	N	N	N	N
vg0130874710	T -> A	LOC_Os01g53720.1	upstream_gene_variant ; 4290.0bp to feature; MODIFIER	silent_mutation	Average:72.642; most accessible tissue: Zhenshan97 flag leaf, score: 85.998	N	N	N	N
vg0130874710	T -> A	LOC_Os01g53710.1	downstream_gene_variant ; 3107.0bp to feature; MODIFIER	silent_mutation	Average:72.642; most accessible tissue: Zhenshan97 flag leaf, score: 85.998	N	N	N	N
vg0130874710	T -> A	LOC_Os01g53710-LOC_Os01g53720	intergenic_region ; MODIFIER	silent_mutation	Average:72.642; most accessible tissue: Zhenshan97 flag leaf, score: 85.998	N	N	N	N
vg0130874710	T -> DEL	N	N	silent_mutation	Average:72.642; most accessible tissue: Zhenshan97 flag leaf, score: 85.998	N	N	N	N
vg0130874710	T -> C	LOC_Os01g53720.2	upstream_gene_variant ; 4290.0bp to feature; MODIFIER	silent_mutation	Average:72.642; most accessible tissue: Zhenshan97 flag leaf, score: 85.998	N	N	N	N
vg0130874710	T -> C	LOC_Os01g53720.1	upstream_gene_variant ; 4290.0bp to feature; MODIFIER	silent_mutation	Average:72.642; most accessible tissue: Zhenshan97 flag leaf, score: 85.998	N	N	N	N
vg0130874710	T -> C	LOC_Os01g53710.1	downstream_gene_variant ; 3107.0bp to feature; MODIFIER	silent_mutation	Average:72.642; most accessible tissue: Zhenshan97 flag leaf, score: 85.998	N	N	N	N
vg0130874710	T -> C	LOC_Os01g53710-LOC_Os01g53720	intergenic_region ; MODIFIER	silent_mutation	Average:72.642; most accessible tissue: Zhenshan97 flag leaf, score: 85.998	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)
vg0130874710	T	A	-0.01	-0.03	-0.02	-0.01	-0.01	0.01
vg0130874710	T	C	0.02	0.0	0.0	0.01	0.02	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0130874710	NA	3.74E-108	mr1008	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
vg0130874710	2.05E-06	2.05E-06	mr1008	Jap_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
vg0130874710	NA	2.56E-106	mr1009	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
vg0130874710	9.49E-07	9.49E-07	mr1009	Jap_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
vg0130874710	NA	5.92E-13	mr1010	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
vg0130874710	NA	1.81E-69	mr1014	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
vg0130874710	NA	1.97E-09	mr1191	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
vg0130874710	NA	1.14E-09	mr1322	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
vg0130874710	NA	5.71E-12	mr1325	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
vg0130874710	NA	7.29E-14	mr1326	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
vg0130874710	NA	8.89E-07	mr1527	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
vg0130874710	NA	7.62E-06	mr1532	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
vg0130874710	NA	2.25E-12	mr1553	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
vg0130874710	NA	8.30E-10	mr1714	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
vg0130874710	NA	5.15E-08	mr1781	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
vg0130874710	NA	1.45E-14	mr1333_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
vg0130874710	NA	1.41E-13	mr1553_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