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Detailed information for vg0316308734:

Variant ID: vg0316308734 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16308734
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTCGCCGCGCCGCGCTCACCCGCCGCCGCCGCTCCTACTCCTCCCAAGTTCGCCTGCCGCCGTCGCTCCTCCCAGGCTCGCTCGCCACCGCTGCTCCT[C/T]
CTAAGCTCGCCTATTATCACCGCTCCGCCCTCCGCGCTCGCCCACCGCGGCCGCTCCTCCTAAGCTCGCCCGTCATCACCGCTCCACCCACCGCCACCAC

Reverse complement sequence

GTGGTGGCGGTGGGTGGAGCGGTGATGACGGGCGAGCTTAGGAGGAGCGGCCGCGGTGGGCGAGCGCGGAGGGCGGAGCGGTGATAATAGGCGAGCTTAG[G/A]
AGGAGCAGCGGTGGCGAGCGAGCCTGGGAGGAGCGACGGCGGCAGGCGAACTTGGGAGGAGTAGGAGCGGCGGCGGCGGGTGAGCGCGGCGCGGCGACAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.00% 9.90% 0.02% 0.00% NA
All Indica  2759 97.50% 2.50% 0.00% 0.00% NA
All Japonica  1512 82.30% 17.60% 0.07% 0.00% NA
Aus  269 53.50% 46.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 96.90% 3.10% 0.00% 0.00% NA
Indica Intermediate  786 95.30% 4.70% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 50.20% 49.60% 0.20% 0.00% NA
Japonica Intermediate  241 94.60% 5.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0316308734 C -> T LOC_Os03g28330.1 upstream_gene_variant ; 1102.0bp to feature; MODIFIER silent_mutation Average:83.0; most accessible tissue: Minghui63 young leaf, score: 91.355 N N N N
vg0316308734 C -> T LOC_Os03g28330.4 upstream_gene_variant ; 2591.0bp to feature; MODIFIER silent_mutation Average:83.0; most accessible tissue: Minghui63 young leaf, score: 91.355 N N N N
vg0316308734 C -> T LOC_Os03g28330.3 upstream_gene_variant ; 2156.0bp to feature; MODIFIER silent_mutation Average:83.0; most accessible tissue: Minghui63 young leaf, score: 91.355 N N N N
vg0316308734 C -> T LOC_Os03g28330.2 upstream_gene_variant ; 2144.0bp to feature; MODIFIER silent_mutation Average:83.0; most accessible tissue: Minghui63 young leaf, score: 91.355 N N N N
vg0316308734 C -> T LOC_Os03g28330.5 upstream_gene_variant ; 1102.0bp to feature; MODIFIER silent_mutation Average:83.0; most accessible tissue: Minghui63 young leaf, score: 91.355 N N N N
vg0316308734 C -> T LOC_Os03g28330-LOC_Os03g28350 intergenic_region ; MODIFIER silent_mutation Average:83.0; most accessible tissue: Minghui63 young leaf, score: 91.355 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)
vg0316308734 C T -0.02 -0.02 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316308734 NA 4.69E-10 mr1047_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
vg0316308734 NA 3.34E-06 mr1072_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
vg0316308734 NA 4.37E-06 mr1075_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
vg0316308734 NA 1.51E-06 mr1077_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
vg0316308734 NA 5.68E-06 mr1269_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
vg0316308734 NA 4.09E-06 mr1291_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
vg0316308734 NA 4.54E-06 mr1295_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
vg0316308734 6.89E-06 NA mr1667_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
vg0316308734 6.98E-07 NA mr1676_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
vg0316308734 NA 6.37E-06 mr1677_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
vg0316308734 NA 2.84E-06 mr1704_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
vg0316308734 NA 3.29E-07 mr1736_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
vg0316308734 NA 3.62E-06 mr1740_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
vg0316308734 4.90E-06 NA mr1758_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
vg0316308734 NA 8.16E-07 mr1786_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
vg0316308734 6.58E-06 NA mr1806_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
vg0316308734 NA 2.84E-07 mr1808_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
vg0316308734 NA 5.94E-07 mr1870_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