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Detailed information for vg0725372439:

Variant ID: vg0725372439 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 25372439
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.57, G: 0.43, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGCGGCGGCGCCGCCGCCGCCGATGGAGCAGGAGCTGGAGCTCCACCGCGACAACGCCGACGACGGCCTCGACGGCCACGTGCGGTGAGAGCTTCTCT[C/G]
TGTGTGTGTGTGGCAAGTCACTTGTGTTCATGAGTTCATCGGCGGTGAGGAGGTGGGCGAGGTCTCGTAGCGTCTCGCCTTTGCGTGGTATTCGGGGTTC

Reverse complement sequence

GAACCCCGAATACCACGCAAAGGCGAGACGCTACGAGACCTCGCCCACCTCCTCACCGCCGATGAACTCATGAACACAAGTGACTTGCCACACACACACA[G/C]
AGAGAAGCTCTCACCGCACGTGGCCGTCGAGGCCGTCGTCGGCGTTGTCGCGGTGGAGCTCCAGCTCCTGCTCCATCGGCGGCGGCGGCGCCGCCGCGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.90% 30.10% 0.04% 0.00% NA
All Indica  2759 94.90% 5.00% 0.07% 0.00% NA
All Japonica  1512 24.10% 75.90% 0.00% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 91.80% 8.10% 0.17% 0.00% NA
Indica II  465 94.00% 6.00% 0.00% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 94.30% 5.60% 0.13% 0.00% NA
Temperate Japonica  767 3.90% 96.10% 0.00% 0.00% NA
Tropical Japonica  504 58.10% 41.90% 0.00% 0.00% NA
Japonica Intermediate  241 17.40% 82.60% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 56.70% 43.30% 0.00% 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
vg0725372439 C -> G LOC_Os07g42395.1 upstream_gene_variant ; 632.0bp to feature; MODIFIER silent_mutation Average:94.82; most accessible tissue: Zhenshan97 flower, score: 97.917 N N N N
vg0725372439 C -> G LOC_Os07g42395.2 upstream_gene_variant ; 583.0bp to feature; MODIFIER silent_mutation Average:94.82; most accessible tissue: Zhenshan97 flower, score: 97.917 N N N N
vg0725372439 C -> G LOC_Os07g42400.1 intron_variant ; MODIFIER silent_mutation Average:94.82; most accessible tissue: Zhenshan97 flower, score: 97.917 N N N N
vg0725372439 C -> G LOC_Os07g42400.2 intron_variant ; MODIFIER silent_mutation Average:94.82; most accessible tissue: Zhenshan97 flower, score: 97.917 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)
vg0725372439 C G -0.01 -0.01 0.0 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0725372439 NA 4.45E-12 mr1386 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
vg0725372439 NA 3.20E-09 mr1563 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
vg0725372439 NA 9.24E-08 mr1825 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
vg0725372439 NA 8.76E-06 mr1170_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
vg0725372439 NA 3.27E-13 mr1178_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
vg0725372439 NA 3.17E-06 mr1498_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
vg0725372439 NA 5.10E-08 mr1563_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
vg0725372439 NA 1.86E-13 mr1769_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