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Detailed information for vg1003374552:

Variant ID: vg1003374552 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3374552
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.64, A: 0.37, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCGTGATGATATGGCAAGCAAGATAATTTGGGGGTGAGCCAACAAATTGCAGTGTGGGGCTTGGATAATGCACTGGTGGTGGATGGAAGATGGAAACT[A/G]
ACAAAGACCTTGAACATATGATGAAGTCCAGGTGGGATGTGAATATGCTAGAAATTGGGTATTGAAGTGGTTGATAAAGAGGGTTATGGTTCTATTCAGA

Reverse complement sequence

TCTGAATAGAACCATAACCCTCTTTATCAACCACTTCAATACCCAATTTCTAGCATATTCACATCCCACCTGGACTTCATCATATGTTCAAGGTCTTTGT[T/C]
AGTTTCCATCTTCCATCCACCACCAGTGCATTATCCAAGCCCCACACTGCAATTTGTTGGCTCACCCCCAAATTATCTTGCTTGCCATATCATCACGCAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.30% 24.30% 1.46% 2.86% NA
All Indica  2759 57.50% 38.50% 1.70% 2.32% NA
All Japonica  1512 95.00% 2.60% 0.66% 1.79% NA
Aus  269 77.70% 3.30% 2.97% 15.99% NA
Indica I  595 53.90% 43.40% 2.02% 0.67% NA
Indica II  465 71.80% 24.70% 1.72% 1.72% NA
Indica III  913 44.60% 49.70% 2.08% 3.61% NA
Indica Intermediate  786 66.80% 29.80% 1.02% 2.42% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 86.10% 6.70% 1.98% 5.16% NA
Japonica Intermediate  241 98.80% 0.80% 0.00% 0.41% NA
VI/Aromatic  96 70.80% 27.10% 1.04% 1.04% NA
Intermediate  90 80.00% 16.70% 3.33% 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
vg1003374552 A -> G LOC_Os10g06550.1 downstream_gene_variant ; 4557.0bp to feature; MODIFIER silent_mutation Average:76.549; most accessible tissue: Callus, score: 90.21 N N N N
vg1003374552 A -> G LOC_Os10g06560.1 downstream_gene_variant ; 2980.0bp to feature; MODIFIER silent_mutation Average:76.549; most accessible tissue: Callus, score: 90.21 N N N N
vg1003374552 A -> G LOC_Os10g06550-LOC_Os10g06560 intergenic_region ; MODIFIER silent_mutation Average:76.549; most accessible tissue: Callus, score: 90.21 N N N N
vg1003374552 A -> DEL N N silent_mutation Average:76.549; most accessible tissue: Callus, score: 90.21 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)
vg1003374552 A G 0.13 0.07 0.05 0.08 0.16 0.2

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003374552 1.40E-11 NA 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
vg1003374552 1.46E-11 1.38E-13 mr1538 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
vg1003374552 4.78E-19 2.19E-23 mr1547 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
vg1003374552 4.53E-17 6.88E-23 mr1547 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
vg1003374552 2.79E-46 2.85E-56 mr1709 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
vg1003374552 7.58E-43 2.63E-69 mr1709 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
vg1003374552 7.18E-14 NA mr1538_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
vg1003374552 4.62E-14 2.40E-20 mr1538_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
vg1003374552 8.65E-22 6.93E-27 mr1547_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
vg1003374552 3.04E-21 2.79E-29 mr1547_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
vg1003374552 9.38E-77 4.44E-99 mr1709_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
vg1003374552 2.60E-66 1.20E-111 mr1709_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