Search for Variation information by Variation ID:

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

Detailed information for vg0900102817:

Variant ID: vg0900102817 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 102817
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTGAATGGTCAGGGAGACCACGAGGGTCAACTTCCCTCCACGAGCGAGCACTGTTGGATGGTCGCTCTGGTCGAAGGTGAGCTTCACCTCCGACCAGCG[C/T]
GCCTTCCGAGTCGCCTCGTGGGTTGGGACGATGGCCAGACGCTCTCGCCTCATGGCCTTGAAGCCTCGGCGGGAGGTGTGAGCCCAAGCCCCCACCTCCC

Reverse complement sequence

GGGAGGTGGGGGCTTGGGCTCACACCTCCCGCCGAGGCTTCAAGGCCATGAGGCGAGAGCGTCTGGCCATCGTCCCAACCCACGAGGCGACTCGGAAGGC[G/A]
CGCTGGTCGGAGGTGAAGCTCACCTTCGACCAGAGCGACCATCCAACAGTGCTCGCTCGTGGAGGGAAGTTGACCCTCGTGGTCTCCCTGACCATTCACA

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	77.80%	5.00%	1.65%	15.55%	NA
All Indica	2759	76.60%	6.90%	2.07%	14.39%	NA
All Japonica	1512	87.40%	0.00%	0.26%	12.37%	NA
Aus	269	48.70%	14.10%	4.83%	32.34%	NA
Indica I	595	84.50%	9.20%	1.68%	4.54%	NA
Indica II	465	71.40%	1.90%	2.80%	23.87%	NA
Indica III	913	72.40%	8.80%	1.64%	17.20%	NA
Indica Intermediate	786	78.60%	6.00%	2.42%	12.98%	NA
Temperate Japonica	767	76.90%	0.00%	0.26%	22.82%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	95.40%	0.00%	0.41%	4.15%	NA
VI/Aromatic	96	37.50%	1.00%	3.12%	58.33%	NA
Intermediate	90	82.20%	7.80%	1.11%	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
vg0900102817	C -> DEL	LOC_Os09g01080.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900102817	C -> T	LOC_Os09g01080.1	synonymous_variant ; p.Ala58Ala; LOW	synonymous_codon	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	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)
vg0900102817	C	T	-0.03	-0.03	-0.03	-0.03	-0.03	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900102817	2.59E-06	NA	mr1570_2	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