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Detailed information for vg0729363250:

Variant ID: vg0729363250 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 29363250
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.55, T: 0.45, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


GATAGATGAGGAGGTAGGGAGGACGGGGAGAAGTAGAGCGAAGAGAAATGAAGCACGTAAAGTATATAGGTTGAAATCATACACGTTGGTGGATACTTAA[T/G]
ACGGATAATATTTTTTAGTATTCCAGTATTGTTAAAGAACCTAGAAATACCAAGAAACACTATAGTATGTATTTACTAGTACTTACCCTCCTTCGATAAA

Reverse complement sequence

TTTATCGAAGGAGGGTAAGTACTAGTAAATACATACTATAGTGTTTCTTGGTATTTCTAGGTTCTTTAACAATACTGGAATACTAAAAAATATTATCCGT[A/C]
TTAAGTATCCACCAACGTGTATGATTTCAACCTATATACTTTACGTGCTTCATTTCTCTTCGCTCTACTTCTCCCCGTCCTCCCTACCTCCTCATCTATC

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 64.00% 35.90% 0.02% 0.00% NA
All Indica  2759 95.20% 4.80% 0.00% 0.00% NA
All Japonica  1512 11.60% 88.40% 0.00% 0.00% NA
Aus  269 65.80% 34.20% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 94.40% 5.60% 0.00% 0.00% NA
Indica III  913 95.30% 4.70% 0.00% 0.00% NA
Indica Intermediate  786 93.30% 6.70% 0.00% 0.00% NA
Temperate Japonica  767 0.90% 99.10% 0.00% 0.00% NA
Tropical Japonica  504 19.60% 80.40% 0.00% 0.00% NA
Japonica Intermediate  241 29.00% 71.00% 0.00% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 43.30% 55.60% 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
vg0729363250 T -> G LOC_Os07g49040.1 upstream_gene_variant ; 402.0bp to feature; MODIFIER silent_mutation Average:73.268; most accessible tissue: Callus, score: 88.805 N N N N
vg0729363250 T -> G LOC_Os07g49030-LOC_Os07g49040 intergenic_region ; MODIFIER silent_mutation Average:73.268; most accessible tissue: Callus, score: 88.805 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)
vg0729363250 T G -0.06 -0.07 -0.05 -0.02 -0.04 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0729363250 NA 6.29E-06 mr1039 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
vg0729363250 NA 1.28E-06 mr1208 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
vg0729363250 1.65E-06 1.65E-06 mr1356 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
vg0729363250 8.66E-06 8.66E-06 mr1544 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
vg0729363250 NA 2.32E-06 mr1785_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
vg0729363250 NA 1.71E-08 mr1837_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