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Detailed information for vg0222477102:

Variant ID: vg0222477102 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22477102
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTGGATTAGCGGTTTGGTTAAATAGTTAATTTGGGTGATATTCCACCGGCCATTAATTGAATCTTTAATTCTTGGTGAACGAAAGCATCTTTAATTGA[G/T]
TAAGAAAGCTCTCACTTTCTCCGTAAAGAAAATGAGAAGAGAATTGAACCAGGAAATGTCTCCCGAATAAAACAAAATTTCCCAGGAATAATCAACCGTC

Reverse complement sequence

GACGGTTGATTATTCCTGGGAAATTTTGTTTTATTCGGGAGACATTTCCTGGTTCAATTCTCTTCTCATTTTCTTTACGGAGAAAGTGAGAGCTTTCTTA[C/A]
TCAATTAAAGATGCTTTCGTTCACCAAGAATTAAAGATTCAATTAATGGCCGGTGGAATATCACCCAAATTAACTATTTAACCAAACCGCTAATCCAGCT

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 46.20% 18.10% 19.21% 16.53% NA
All Indica  2759 21.30% 26.20% 29.39% 23.12% NA
All Japonica  1512 95.80% 1.00% 1.72% 1.46% NA
Aus  269 0.40% 38.30% 21.56% 39.78% NA
Indica I  595 18.30% 21.20% 41.01% 19.50% NA
Indica II  465 10.50% 24.50% 33.55% 31.40% NA
Indica III  913 28.30% 29.50% 22.67% 19.61% NA
Indica Intermediate  786 21.90% 27.10% 25.95% 25.06% NA
Temperate Japonica  767 99.50% 0.00% 0.26% 0.26% NA
Tropical Japonica  504 89.30% 2.20% 4.76% 3.77% NA
Japonica Intermediate  241 97.90% 1.70% 0.00% 0.41% NA
VI/Aromatic  96 88.50% 2.10% 3.12% 6.25% NA
Intermediate  90 65.60% 14.40% 11.11% 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
vg0222477102 G -> T LOC_Os02g37170.1 upstream_gene_variant ; 4992.0bp to feature; MODIFIER silent_mutation Average:75.417; most accessible tissue: Minghui63 flower, score: 88.094 N N N N
vg0222477102 G -> T LOC_Os02g37180.1 upstream_gene_variant ; 1511.0bp to feature; MODIFIER silent_mutation Average:75.417; most accessible tissue: Minghui63 flower, score: 88.094 N N N N
vg0222477102 G -> T LOC_Os02g37190.1 downstream_gene_variant ; 680.0bp to feature; MODIFIER silent_mutation Average:75.417; most accessible tissue: Minghui63 flower, score: 88.094 N N N N
vg0222477102 G -> T LOC_Os02g37200.1 downstream_gene_variant ; 4546.0bp to feature; MODIFIER silent_mutation Average:75.417; most accessible tissue: Minghui63 flower, score: 88.094 N N N N
vg0222477102 G -> T LOC_Os02g37180-LOC_Os02g37190 intergenic_region ; MODIFIER silent_mutation Average:75.417; most accessible tissue: Minghui63 flower, score: 88.094 N N N N
vg0222477102 G -> DEL N N silent_mutation Average:75.417; most accessible tissue: Minghui63 flower, score: 88.094 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)
vg0222477102 G T 0.02 -0.01 -0.03 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222477102 5.19E-06 1.45E-16 mr1069 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
vg0222477102 NA 4.07E-06 mr1069 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
vg0222477102 NA 5.75E-32 mr1072 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
vg0222477102 NA 3.32E-07 mr1072 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
vg0222477102 1.25E-07 1.80E-37 mr1075 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
vg0222477102 2.45E-07 4.07E-10 mr1075 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
vg0222477102 NA 4.61E-21 mr1077 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
vg0222477102 NA 8.15E-07 mr1077 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
vg0222477102 8.29E-07 1.02E-44 mr1124 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
vg0222477102 NA 7.36E-09 mr1124 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
vg0222477102 NA 2.92E-16 mr1146 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
vg0222477102 NA 4.76E-16 mr1149 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
vg0222477102 NA 2.91E-23 mr1150 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
vg0222477102 6.22E-06 2.12E-35 mr1202 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
vg0222477102 NA 2.04E-07 mr1202 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
vg0222477102 NA 6.84E-10 mr1222 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
vg0222477102 NA 7.31E-13 mr1239 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
vg0222477102 7.56E-06 4.10E-17 mr1441 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
vg0222477102 4.45E-06 8.78E-18 mr1592 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
vg0222477102 8.93E-06 1.29E-53 mr1861 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
vg0222477102 NA 5.05E-07 mr1861 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
vg0222477102 NA 1.01E-07 mr1962 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
vg0222477102 8.98E-07 8.63E-44 mr1072_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
vg0222477102 1.89E-07 6.45E-46 mr1075_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
vg0222477102 NA 3.16E-07 mr1075_2 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
vg0222477102 NA 4.32E-24 mr1077_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
vg0222477102 NA 2.32E-22 mr1095_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
vg0222477102 NA 1.84E-06 mr1095_2 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
vg0222477102 NA 1.10E-06 mr1099_2 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
vg0222477102 9.36E-08 2.21E-62 mr1124_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
vg0222477102 NA 9.26E-11 mr1124_2 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
vg0222477102 4.10E-06 2.05E-31 mr1149_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
vg0222477102 NA 2.11E-35 mr1150_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
vg0222477102 NA 1.79E-11 mr1222_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
vg0222477102 NA 4.10E-07 mr1222_2 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
vg0222477102 8.82E-06 1.24E-31 mr1441_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
vg0222477102 NA 4.55E-19 mr1592_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
vg0222477102 NA 2.75E-14 mr1595_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
vg0222477102 NA 4.00E-12 mr1600_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
vg0222477102 5.97E-06 NA mr1911_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
vg0222477102 4.17E-06 3.68E-07 mr1911_2 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
vg0222477102 NA 1.20E-06 mr1918_2 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