Search for Variation information by Variation ID:

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

Detailed information for vg0701484527:

Variant ID: vg0701484527 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 1484527
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAATTGCTAGGTTTGTTTCTTGAGAAAAAACATTCCATTTTGTATGTGGGCTGATCAGCCATCAGCGCCTATTTGAATGTTTTTTTTGTCCTCCTCTAT[C/T]
CATTTCTTAGAGTTTTGAGCTGATTCTTTGGTATTTTTCTGAAGTTCACAACCCATCCTTATATGGATACATGTCTCCTTCACTTTAGTATGATTTTCCT

Reverse complement sequence

AGGAAAATCATACTAAAGTGAAGGAGACATGTATCCATATAAGGATGGGTTGTGAACTTCAGAAAAATACCAAAGAATCAGCTCAAAACTCTAAGAAATG[G/A]
ATAGAGGAGGACAAAAAAAACATTCAAATAGGCGCTGATGGCTGATCAGCCCACATACAAAATGGAATGTTTTTTCTCAAGAAACAAACCTAGCAATTGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.40%	20.10%	0.15%	37.35%	NA
All Indica	2759	63.10%	8.00%	0.22%	28.63%	NA
All Japonica	1512	3.40%	45.50%	0.07%	51.06%	NA
Aus	269	35.70%	1.10%	0.00%	63.20%	NA
Indica I	595	92.90%	6.40%	0.00%	0.67%	NA
Indica II	465	13.10%	6.50%	0.65%	79.78%	NA
Indica III	913	72.00%	10.40%	0.00%	17.63%	NA
Indica Intermediate	786	59.80%	7.50%	0.38%	32.32%	NA
Temperate Japonica	767	1.40%	76.70%	0.00%	21.90%	NA
Tropical Japonica	504	6.20%	5.60%	0.20%	88.10%	NA
Japonica Intermediate	241	3.70%	29.90%	0.00%	66.39%	NA
VI/Aromatic	96	86.50%	7.30%	0.00%	6.25%	NA
Intermediate	90	38.90%	31.10%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0701484527	C -> DEL	N	N	silent_mutation	Average:46.374; most accessible tissue: Callus, score: 93.264	N	N	N	N
vg0701484527	C -> T	LOC_Os07g03670.1	upstream_gene_variant ; 1127.0bp to feature; MODIFIER	silent_mutation	Average:46.374; most accessible tissue: Callus, score: 93.264	N	N	N	N
vg0701484527	C -> T	LOC_Os07g03650-LOC_Os07g03670	intergenic_region ; MODIFIER	silent_mutation	Average:46.374; most accessible tissue: Callus, score: 93.264	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)
vg0701484527	C	T	-0.07	-0.03	-0.02	-0.04	-0.06	-0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0701484527	NA	1.28E-09	mr1005	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
vg0701484527	2.57E-06	4.29E-06	mr1418	Ind_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
vg0701484527	1.55E-06	1.55E-06	mr1420	Ind_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
vg0701484527	8.40E-06	8.40E-06	mr1488	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
vg0701484527	7.84E-06	7.84E-06	mr1747	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
vg0701484527	2.37E-07	2.37E-07	mr1812	Ind_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