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Detailed information for vg0330758408:

Variant ID: vg0330758408 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 30758408
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTGAGAGAACTGAATGTTTTCTCATGTTTCATAAATTAGGCTTCGATTATTTTTTAAACCTTTGACCTACTGTTACAAGTAACAATATAATCAAGCTG[T/G]
CAACGAATAGCGAAGTGAGCGTAGCTCAGTCGATTAGGTTTCTTATGGTGGAATCAGTTCACCCGTATTTAAATTCTAGATTTGAGACGAGTGCTTACAT

Reverse complement sequence

ATGTAAGCACTCGTCTCAAATCTAGAATTTAAATACGGGTGAACTGATTCCACCATAAGAAACCTAATCGACTGAGCTACGCTCACTTCGCTATTCGTTG[A/C]
CAGCTTGATTATATTGTTACTTGTAACAGTAGGTCAAAGGTTTAAAAAATAATCGAAGCCTAATTTATGAAACATGAGAAAACATTCAGTTCTCTCAACT

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 64.20% 34.70% 1.06% 0.00% NA
All Indica  2759 78.40% 21.10% 0.43% 0.00% NA
All Japonica  1512 35.50% 62.30% 2.18% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 62.60% 36.60% 0.86% 0.00% NA
Indica III  913 70.90% 28.60% 0.55% 0.00% NA
Indica Intermediate  786 81.40% 18.20% 0.38% 0.00% NA
Temperate Japonica  767 9.30% 89.20% 1.56% 0.00% NA
Tropical Japonica  504 81.00% 15.90% 3.17% 0.00% NA
Japonica Intermediate  241 24.10% 73.90% 2.07% 0.00% NA
VI/Aromatic  96 17.70% 81.20% 1.04% 0.00% NA
Intermediate  90 53.30% 42.20% 4.44% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0330758408 T -> G LOC_Os03g53640.1 upstream_gene_variant ; 898.0bp to feature; MODIFIER silent_mutation Average:73.795; most accessible tissue: Zhenshan97 root, score: 91.119 N N N N
vg0330758408 T -> G LOC_Os03g53650.1 upstream_gene_variant ; 1596.0bp to feature; MODIFIER silent_mutation Average:73.795; most accessible tissue: Zhenshan97 root, score: 91.119 N N N N
vg0330758408 T -> G LOC_Os03g53650.4 upstream_gene_variant ; 1596.0bp to feature; MODIFIER silent_mutation Average:73.795; most accessible tissue: Zhenshan97 root, score: 91.119 N N N N
vg0330758408 T -> G LOC_Os03g53650.3 upstream_gene_variant ; 1596.0bp to feature; MODIFIER silent_mutation Average:73.795; most accessible tissue: Zhenshan97 root, score: 91.119 N N N N
vg0330758408 T -> G LOC_Os03g53650.2 upstream_gene_variant ; 1596.0bp to feature; MODIFIER silent_mutation Average:73.795; most accessible tissue: Zhenshan97 root, score: 91.119 N N N N
vg0330758408 T -> G LOC_Os03g53630.1 downstream_gene_variant ; 3280.0bp to feature; MODIFIER silent_mutation Average:73.795; most accessible tissue: Zhenshan97 root, score: 91.119 N N N N
vg0330758408 T -> G LOC_Os03g53640-LOC_Os03g53650 intergenic_region ; MODIFIER silent_mutation Average:73.795; most accessible tissue: Zhenshan97 root, score: 91.119 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)
vg0330758408 T G -0.13 -0.09 -0.06 -0.01 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0330758408 7.09E-06 2.84E-11 mr1050 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
vg0330758408 NA 3.10E-10 mr1050 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
vg0330758408 NA 4.74E-12 mr1272 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
vg0330758408 2.09E-06 8.82E-12 mr1272 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
vg0330758408 NA 2.69E-07 mr1354 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
vg0330758408 NA 1.64E-08 mr1551 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
vg0330758408 NA 4.17E-06 mr1595 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
vg0330758408 NA 1.74E-11 mr1607 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
vg0330758408 NA 1.59E-06 mr1644 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
vg0330758408 NA 4.49E-08 mr1699 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
vg0330758408 NA 8.98E-11 mr1829 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
vg0330758408 3.64E-08 4.72E-19 mr1829 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
vg0330758408 NA 1.10E-11 mr1842 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
vg0330758408 NA 3.55E-13 mr1902 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
vg0330758408 NA 1.10E-11 mr1902 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
vg0330758408 NA 5.74E-09 mr1935 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
vg0330758408 NA 4.09E-09 mr1036_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
vg0330758408 NA 2.53E-12 mr1050_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
vg0330758408 1.96E-07 2.61E-12 mr1050_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
vg0330758408 NA 2.07E-07 mr1159_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
vg0330758408 NA 6.49E-06 mr1169_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
vg0330758408 NA 2.42E-06 mr1174_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
vg0330758408 NA 2.03E-07 mr1272_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
vg0330758408 NA 4.79E-06 mr1272_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
vg0330758408 NA 4.17E-08 mr1304_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
vg0330758408 NA 3.98E-07 mr1308_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
vg0330758408 NA 1.97E-07 mr1354_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
vg0330758408 NA 3.93E-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
vg0330758408 NA 7.77E-10 mr1551_2 Jap_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
vg0330758408 NA 1.09E-07 mr1607_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
vg0330758408 NA 8.57E-09 mr1699_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
vg0330758408 NA 1.66E-07 mr1707_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
vg0330758408 NA 8.51E-06 mr1806_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
vg0330758408 NA 1.25E-10 mr1829_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
vg0330758408 2.96E-07 1.43E-20 mr1829_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
vg0330758408 NA 2.56E-12 mr1842_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
vg0330758408 NA 3.34E-16 mr1902_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
vg0330758408 NA 4.37E-16 mr1902_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
vg0330758408 NA 9.86E-07 mr1933_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
vg0330758408 NA 1.72E-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