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Search for Variation information by Variation ID:

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

Detailed information for vg0501780209:

Variant ID: vg0501780209 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1780209
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.09, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTTTTTTCATTTTTATTGTTTCTTTGGCTAAAGTTAATCCCTATATTTTCTCCCGAATCTAGTGCCATGTATATCCCCAAATCAATCCCCAAATCCC[C/T]
CGATTCAAAGTAACATCCCAAATCTTAAGTTACATATACACACAAATCAAATACATCACAAATCCTAAAAAAATACGCACAAATCAGATACATCAAAAAT

Reverse complement sequence

ATTTTTGATGTATCTGATTTGTGCGTATTTTTTTAGGATTTGTGATGTATTTGATTTGTGTGTATATGTAACTTAAGATTTGGGATGTTACTTTGAATCG[G/A]
GGGATTTGGGGATTGATTTGGGGATATACATGGCACTAGATTCGGGAGAAAATATAGGGATTAACTTTAGCCAAAGAAACAATAAAAATGAAAAAAAAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.20% 15.30% 0.44% 17.05% NA
All Indica  2759 78.40% 15.80% 0.11% 5.69% NA
All Japonica  1512 55.60% 1.80% 1.12% 41.53% NA
Aus  269 11.50% 88.10% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 83.20% 13.30% 0.00% 3.44% NA
Indica III  913 57.60% 30.00% 0.11% 12.27% NA
Indica Intermediate  786 83.50% 12.60% 0.25% 3.69% NA
Temperate Japonica  767 69.60% 0.80% 0.26% 29.34% NA
Tropical Japonica  504 38.50% 3.60% 1.98% 55.95% NA
Japonica Intermediate  241 46.50% 1.20% 2.07% 50.21% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 61.10% 15.60% 0.00% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0501780209 C -> T LOC_Os05g03960.1 upstream_gene_variant ; 1932.0bp to feature; MODIFIER silent_mutation Average:42.701; most accessible tissue: Minghui63 young leaf, score: 96.323 N N N N
vg0501780209 C -> T LOC_Os05g03950.1 downstream_gene_variant ; 2550.0bp to feature; MODIFIER silent_mutation Average:42.701; most accessible tissue: Minghui63 young leaf, score: 96.323 N N N N
vg0501780209 C -> T LOC_Os05g03972.1 downstream_gene_variant ; 4927.0bp to feature; MODIFIER silent_mutation Average:42.701; most accessible tissue: Minghui63 young leaf, score: 96.323 N N N N
vg0501780209 C -> T LOC_Os05g03950-LOC_Os05g03960 intergenic_region ; MODIFIER silent_mutation Average:42.701; most accessible tissue: Minghui63 young leaf, score: 96.323 N N N N
vg0501780209 C -> DEL N N silent_mutation Average:42.701; most accessible tissue: Minghui63 young leaf, score: 96.323 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)
vg0501780209 C T -0.02 -0.01 -0.01 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501780209 NA 3.02E-06 mr1028 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
vg0501780209 NA 5.03E-07 mr1113 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
vg0501780209 NA 8.23E-09 mr1114 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
vg0501780209 NA 2.02E-07 mr1116 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
vg0501780209 3.01E-09 2.53E-12 mr1117 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
vg0501780209 7.84E-07 2.59E-10 mr1119 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
vg0501780209 NA 6.49E-06 mr1120 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
vg0501780209 1.18E-06 NA mr1242 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
vg0501780209 NA 9.17E-08 mr1247 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
vg0501780209 NA 5.52E-06 mr1262 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
vg0501780209 NA 2.43E-06 mr1365 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
vg0501780209 NA 4.24E-07 mr1369 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
vg0501780209 NA 2.40E-07 mr1382 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
vg0501780209 NA 3.58E-06 mr1393 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
vg0501780209 NA 1.50E-11 mr1409 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
vg0501780209 NA 3.99E-07 mr1453 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
vg0501780209 NA 7.86E-12 mr1522 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
vg0501780209 NA 2.58E-06 mr1545 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
vg0501780209 NA 1.05E-06 mr1556 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
vg0501780209 NA 1.19E-08 mr1574 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
vg0501780209 NA 1.63E-11 mr1649 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
vg0501780209 NA 1.68E-08 mr1866 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
vg0501780209 NA 2.53E-07 mr1917 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
vg0501780209 NA 5.95E-06 mr1952 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
vg0501780209 1.84E-06 1.07E-08 mr1113_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
vg0501780209 4.19E-06 1.95E-08 mr1114_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
vg0501780209 1.99E-06 1.00E-08 mr1117_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
vg0501780209 NA 8.50E-08 mr1119_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
vg0501780209 NA 1.66E-06 mr1120_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
vg0501780209 NA 4.85E-07 mr1247_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
vg0501780209 NA 5.67E-07 mr1522_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