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Detailed information for vg0708430086:

Variant ID: vg0708430086 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 8430086
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.17, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


CTGGGCGTCGGATGGGAAGGGAGGAGGGGGAGGAGAGGGCCGGGATGGGAGGAGGAAGGGGAGGAGGAGGAGGAGAGGGAGATGGATCTGAGGAGAGATC[A/G]
GATGGGAAGGGAGGGGGAAGGAGAGTGCCGGGATGGGAGGAGGAAGAGGAGAGGGAGATGGATCTGAGGAGAGGAGAGGCCGGTTGTTGGTGAGAGGATA

Reverse complement sequence

TATCCTCTCACCAACAACCGGCCTCTCCTCTCCTCAGATCCATCTCCCTCTCCTCTTCCTCCTCCCATCCCGGCACTCTCCTTCCCCCTCCCTTCCCATC[T/C]
GATCTCTCCTCAGATCCATCTCCCTCTCCTCCTCCTCCTCCCCTTCCTCCTCCCATCCCGGCCCTCTCCTCCCCCTCCTCCCTTCCCATCCGACGCCCAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.50% 35.40% 0.68% 1.42% NA
All Indica  2759 94.30% 2.30% 1.01% 2.39% NA
All Japonica  1512 12.70% 87.20% 0.07% 0.07% NA
Aus  269 34.60% 64.70% 0.74% 0.00% NA
Indica I  595 98.20% 0.50% 1.01% 0.34% NA
Indica II  465 92.70% 5.20% 0.86% 1.29% NA
Indica III  913 98.70% 1.00% 0.00% 0.33% NA
Indica Intermediate  786 87.20% 3.60% 2.29% 7.00% NA
Temperate Japonica  767 16.00% 83.70% 0.13% 0.13% NA
Tropical Japonica  504 11.50% 88.50% 0.00% 0.00% NA
Japonica Intermediate  241 4.60% 95.40% 0.00% 0.00% NA
VI/Aromatic  96 22.90% 77.10% 0.00% 0.00% NA
Intermediate  90 53.30% 45.60% 1.11% 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
vg0708430086 A -> DEL LOC_Os07g14760.1 N frameshift_variant Average:78.107; most accessible tissue: Minghui63 young leaf, score: 91.355 N N N N
vg0708430086 A -> G LOC_Os07g14760.1 synonymous_variant ; p.Ser85Ser; LOW synonymous_codon Average:78.107; most accessible tissue: Minghui63 young leaf, score: 91.355 N N N N
vg0708430086 A -> G LOC_Os07g14760.1 synonymous_variant ; p.Ser85Ser; LOW nonsynonymous_codon ; S85P Average:78.107; most accessible tissue: Minghui63 young leaf, score: 91.355 unknown unknown TOLERATED 0.22

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)
vg0708430086 A G -0.02 -0.02 -0.02 -0.02 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0708430086 NA 5.90E-08 mr1666 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
vg0708430086 NA 1.27E-08 mr1827 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
vg0708430086 NA 5.00E-07 mr1161_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
vg0708430086 2.18E-06 4.18E-07 mr1180_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
vg0708430086 NA 1.99E-22 mr1316_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
vg0708430086 NA 7.41E-19 mr1581_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