Search for Variation information by Variation ID:

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

Detailed information for vg1207647527:

Variant ID: vg1207647527 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7647527
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCAGTCTGATTTTCGTTCCTTGATCACAAAACCGGGTACTACAGGTCCCCGAACTTATGAAACCGTTTAAATAAGGTCCCTTGGCAGTATTTGACTCCG[G/T]
TTTTGGGTGAGGTGGCGCCTACGTGACTAATTAACTCGGTCTTCATCTGACGTGGCATTGACGTGGCACTTACGTGGCAATTCGATCCGAAAAATAATAA

Reverse complement sequence

TTATTATTTTTCGGATCGAATTGCCACGTAAGTGCCACGTCAATGCCACGTCAGATGAAGACCGAGTTAATTAGTCACGTAGGCGCCACCTCACCCAAAA[C/A]
CGGAGTCAAATACTGCCAAGGGACCTTATTTAAACGGTTTCATAAGTTCGGGGACCTGTAGTACCCGGTTTTGTGATCAAGGAACGAAAATCAGACTGGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.50%	4.70%	0.76%	3.05%	NA
All Indica	2759	94.60%	0.20%	0.04%	5.15%	NA
All Japonica	1512	84.20%	13.70%	2.12%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	84.40%	0.00%	0.00%	15.63%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	97.90%	0.10%	0.00%	1.97%	NA
Indica Intermediate	786	95.50%	0.40%	0.13%	3.94%	NA
Temperate Japonica	767	96.00%	2.00%	2.09%	0.00%	NA
Tropical Japonica	504	62.90%	34.30%	2.78%	0.00%	NA
Japonica Intermediate	241	91.30%	7.90%	0.83%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	85.60%	10.00%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207647527	G -> DEL	N	N	silent_mutation	Average:85.724; most accessible tissue: Minghui63 panicle, score: 97.507	N	N	N	N
vg1207647527	G -> T	LOC_Os12g13590.1	upstream_gene_variant ; 3233.0bp to feature; MODIFIER	silent_mutation	Average:85.724; most accessible tissue: Minghui63 panicle, score: 97.507	N	N	N	N
vg1207647527	G -> T	LOC_Os12g13610.1	upstream_gene_variant ; 2215.0bp to feature; MODIFIER	silent_mutation	Average:85.724; most accessible tissue: Minghui63 panicle, score: 97.507	N	N	N	N
vg1207647527	G -> T	LOC_Os12g13600.1	downstream_gene_variant ; 407.0bp to feature; MODIFIER	silent_mutation	Average:85.724; most accessible tissue: Minghui63 panicle, score: 97.507	N	N	N	N
vg1207647527	G -> T	LOC_Os12g13590-LOC_Os12g13600	intergenic_region ; MODIFIER	silent_mutation	Average:85.724; most accessible tissue: Minghui63 panicle, score: 97.507	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)
vg1207647527	G	T	0.02	0.01	0.01	0.02	0.04	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207647527	NA	3.34E-06	mr1156	Jap_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
vg1207647527	NA	1.69E-06	mr1422	Jap_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
vg1207647527	NA	7.30E-09	mr1361_2	Jap_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
vg1207647527	NA	3.95E-06	mr1398_2	Jap_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
vg1207647527	8.59E-06	NA	mr1422_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
vg1207647527	NA	3.45E-09	mr1422_2	Jap_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
vg1207647527	3.84E-09	NA	mr1850_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
vg1207647527	NA	2.43E-09	mr1942_2	Jap_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