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Detailed information for vg0211759191:

Variant ID: vg0211759191 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 11759191
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCAACGGCGGCGGCGGATAAGGAGGATACGAGCATGGCGTTGGTGCTGGCTAGCACCGATGCGATACGAGGTTAGCGAAGCCATCTCTTGTTGGTTCT[T/G]
ATTGGTTTGGGGCTAATTTTTGCCTCGAGAAAATCACTGCTCCAGATGCTCTCTTTTGCTCTTGCTCTCGTTGTGTATGGGGAATTGCCTCCTCGAGTTC

Reverse complement sequence

GAACTCGAGGAGGCAATTCCCCATACACAACGAGAGCAAGAGCAAAAGAGAGCATCTGGAGCAGTGATTTTCTCGAGGCAAAAATTAGCCCCAAACCAAT[A/C]
AGAACCAACAAGAGATGGCTTCGCTAACCTCGTATCGCATCGGTGCTAGCCAGCACCAACGCCATGCTCGTATCCTCCTTATCCGCCGCCGCCGTTGCCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.40% 39.00% 4.55% 5.08% NA
All Indica  2759 80.90% 4.10% 6.89% 8.19% NA
All Japonica  1512 1.50% 98.20% 0.26% 0.07% NA
Aus  269 52.40% 38.30% 5.20% 4.09% NA
Indica I  595 85.00% 0.30% 11.26% 3.36% NA
Indica II  465 81.90% 2.80% 7.31% 7.96% NA
Indica III  913 80.90% 5.10% 1.75% 12.16% NA
Indica Intermediate  786 77.00% 6.40% 9.29% 7.38% NA
Temperate Japonica  767 0.80% 99.00% 0.26% 0.00% NA
Tropical Japonica  504 2.60% 97.20% 0.20% 0.00% NA
Japonica Intermediate  241 1.20% 97.90% 0.41% 0.41% NA
VI/Aromatic  96 0.00% 100.00% 0.00% 0.00% NA
Intermediate  90 36.70% 53.30% 7.78% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0211759191 T -> G LOC_Os02g19980.1 downstream_gene_variant ; 1608.0bp to feature; MODIFIER silent_mutation Average:84.739; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0211759191 T -> G LOC_Os02g19990.1 intron_variant ; MODIFIER silent_mutation Average:84.739; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0211759191 T -> G LOC_Os02g19990.2 intron_variant ; MODIFIER silent_mutation Average:84.739; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0211759191 T -> DEL N N silent_mutation Average:84.739; most accessible tissue: Zhenshan97 panicle, score: 89.389 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)
vg0211759191 T G 0.01 0.01 0.01 0.0 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0211759191 NA 1.18E-49 mr1125 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
vg0211759191 NA 1.72E-15 mr1156 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
vg0211759191 2.32E-06 NA mr1275 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
vg0211759191 NA 1.20E-26 mr1309 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
vg0211759191 NA 6.39E-10 mr1342 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
vg0211759191 NA 1.60E-31 mr1448 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
vg0211759191 NA 1.39E-85 mr1517 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
vg0211759191 NA 2.41E-39 mr1534 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
vg0211759191 NA 1.22E-72 mr1536 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
vg0211759191 NA 2.63E-70 mr1538 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
vg0211759191 NA 3.49E-17 mr1566 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
vg0211759191 NA 5.30E-11 mr1713 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
vg0211759191 NA 2.44E-36 mr1733 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
vg0211759191 NA 1.01E-29 mr1737 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
vg0211759191 NA 2.09E-53 mr1795 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
vg0211759191 NA 1.45E-39 mr1890 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
vg0211759191 NA 3.42E-07 mr1915 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
vg0211759191 NA 1.08E-12 mr1514_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