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Detailed information for vg0323995709:

Variant ID: vg0323995709 (JBrowse)	Variation Type: INDEL
Chromosome: chr03	Position: 23995709
Reference Allele: TATGTTTAAAAAAGTCAACGGTGTCAAACCTTCCATAAC	Alternative Allele: CATGTTTAAAAAAGTCAACGGTGTCAAACCTTCCATAAC,T
Primary Allele: TATGTTTAAAAAAGTCAACG GTGTCAAACCTTCCATAAC	Secondary Allele: CATGTTTAAAAAAGTCAACG GTGTCAAACCTTCCATAAC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTCTTTTTCTATCATTTGATTTATTGTTAAATATACTTTTATGTATACATATAATTTTACACATATCACAAAAGTTTTTAAATAAGACAAACGGTCAAA[TATGTTTAAAAAAGTCAACGGTGTCAAACCTTCCATAAC/CATGTTTAAAAAAGTCAACGGTGTCAAACCTTCCATAAC,T]
ATTTAGGGAAGGAGGTAGTATTTGGCTGGCAAGGTGACATGGCCACCATGTGCTGCCTTGCTCTTATGCACAGTAGGAGTATCGCTATGGCTTGTTCTTT

Reverse complement sequence

AAAGAACAAGCCATAGCGATACTCCTACTGTGCATAAGAGCAAGGCAGCACATGGTGGCCATGTCACCTTGCCAGCCAAATACTACCTCCTTCCCTAAAT[GTTATGGAAGGTTTGACACCGTTGACTTTTTTAAACATA/GTTATGGAAGGTTTGACACCGTTGACTTTTTTAAACATG,A]
TTTGACCGTTTGTCTTATTTAAAAACTTTTGTGATATGTGTAAAATTATATGTATACATAAAAGTATATTTAACAATAAATCAAATGATAGAAAAAGAAT

Allele Frequencies:

Populations	Population Size	Frequency of TATGTTTAAAAAAGTCAACG GTGTCAAACCTTCCATAAC(primary allele)	Frequency of CATGTTTAAAAAAGTCAACG GTGTCAAACCTTCCATAAC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.50%	24.50%	17.18%	21.65%	T: 1.16%
All Indica	2759	1.90%	34.90%	28.02%	35.01%	T: 0.14%
All Japonica	1512	99.10%	0.40%	0.13%	0.33%	NA
Aus	269	5.60%	53.90%	9.29%	13.01%	T: 18.22%
Indica I	595	0.80%	44.40%	36.30%	18.49%	NA
Indica II	465	1.30%	33.30%	32.04%	32.90%	T: 0.43%
Indica III	913	1.40%	29.60%	19.39%	49.62%	NA
Indica Intermediate	786	3.70%	34.90%	29.39%	31.81%	T: 0.25%
Temperate Japonica	767	99.50%	0.10%	0.00%	0.39%	NA
Tropical Japonica	504	99.00%	0.60%	0.20%	0.20%	NA
Japonica Intermediate	241	98.30%	0.80%	0.41%	0.41%	NA
VI/Aromatic	96	71.90%	21.90%	4.17%	2.08%	NA
Intermediate	90	46.70%	25.60%	8.89%	16.67%	T: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0323995709	TATGTTTAAAAAAGTCAACGGTGTCAAACCTTCCATAAC -> T	LOC_Os03g43020.1	downstream_gene_variant ; 3502.0bp to feature; MODIFIER	silent_mutation	Average:68.122; most accessible tissue: Zhenshan97 flower, score: 87.963	N	N	N	N
vg0323995709	TATGTTTAAAAAAGTCAACGGTGTCAAACCTTCCATAAC -> T	LOC_Os03g43010.1	intron_variant ; MODIFIER	silent_mutation	Average:68.122; most accessible tissue: Zhenshan97 flower, score: 87.963	N	N	N	N
vg0323995709	TATGTTTAAAAAAGTCAACGGTGTCAAACCTTCCATAAC -> DEL	N	N	silent_mutation	Average:68.122; most accessible tissue: Zhenshan97 flower, score: 87.963	N	N	N	N
vg0323995709	TATGTTTAAAAAAGTCAACGGTGTCAAACCTTCCATAAC -> CATGTTTAAAAAAGTCAACGGTGTCAAACC TTCCATAAC	LOC_Os03g43020.1	downstream_gene_variant ; 3503.0bp to feature; MODIFIER	silent_mutation	Average:68.122; most accessible tissue: Zhenshan97 flower, score: 87.963	N	N	N	N
vg0323995709	TATGTTTAAAAAAGTCAACGGTGTCAAACCTTCCATAAC -> CATGTTTAAAAAAGTCAACGGTGTCAAACC TTCCATAAC	LOC_Os03g43010.1	intron_variant ; MODIFIER	silent_mutation	Average:68.122; most accessible tissue: Zhenshan97 flower, score: 87.963	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)
vg0323995709	TATGT*	CATGT*	-0.01	-0.04	-0.02	-0.03	-0.04	-0.03
vg0323995709	TATGT*	T	-0.11	-0.05	-0.04	0.2	0.24	0.1

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0323995709	4.36E-06	NA	mr1248	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
vg0323995709	NA	7.99E-26	mr1632	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
vg0323995709	NA	1.16E-80	mr1718	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
vg0323995709	NA	2.20E-119	mr1750	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
vg0323995709	NA	2.06E-14	mr1133_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
vg0323995709	NA	3.23E-21	mr1698_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
vg0323995709	NA	2.64E-110	mr1718_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
vg0323995709	NA	9.57E-153	mr1750_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
vg0323995709	NA	1.70E-33	mr1873_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
vg0323995709	NA	3.88E-41	mr1944_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