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Detailed information for vg1009694705:

Variant ID: vg1009694705 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9694705
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCCACCAAAGTCACCAAGGAATTAAGAGGGAATGACAGGCGGTGTCCCCCGTGTCAGGCGGAGGACGGTACTGGGACCCACCTGAGGACAAGCAACCAC[C/T]
TTGCTTCCGGTTGAAGGCATGGATGTTGACGTGACCAGGGGTGTGTGGGCCCCCCTCCAATGATGAGTTATTTAAAGTCGGTGCATGTGGTATCCCCTTC

Reverse complement sequence

GAAGGGGATACCACATGCACCGACTTTAAATAACTCATCATTGGAGGGGGGCCCACACACCCCTGGTCACGTCAACATCCATGCCTTCAACCGGAAGCAA[G/A]
GTGGTTGCTTGTCCTCAGGTGGGTCCCAGTACCGTCCTCCGCCTGACACGGGGGACACCGCCTGTCATTCCCTCTTAATTCCTTGGTGACTTTGGTGGAC

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 75.80% 23.80% 0.17% 0.21% NA
All Indica  2759 61.60% 38.10% 0.11% 0.14% NA
All Japonica  1512 96.00% 3.30% 0.33% 0.40% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 75.10% 24.20% 0.17% 0.50% NA
Indica II  465 42.20% 57.60% 0.22% 0.00% NA
Indica III  913 66.40% 33.60% 0.00% 0.00% NA
Indica Intermediate  786 57.40% 42.40% 0.13% 0.13% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 89.90% 8.10% 0.79% 1.19% NA
Japonica Intermediate  241 97.90% 1.70% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg1009694705 C -> T LOC_Os10g19030.1 downstream_gene_variant ; 3320.0bp to feature; MODIFIER silent_mutation Average:79.987; most accessible tissue: Zhenshan97 young leaf, score: 94.617 N N N N
vg1009694705 C -> T LOC_Os10g19040.1 downstream_gene_variant ; 2037.0bp to feature; MODIFIER silent_mutation Average:79.987; most accessible tissue: Zhenshan97 young leaf, score: 94.617 N N N N
vg1009694705 C -> T LOC_Os10g19030-LOC_Os10g19040 intergenic_region ; MODIFIER silent_mutation Average:79.987; most accessible tissue: Zhenshan97 young leaf, score: 94.617 N N N N
vg1009694705 C -> DEL N N silent_mutation Average:79.987; most accessible tissue: Zhenshan97 young leaf, score: 94.617 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)
vg1009694705 C T -0.03 -0.03 -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
vg1009694705 9.65E-07 1.50E-10 mr1053 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
vg1009694705 5.25E-07 5.86E-07 mr1053 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
vg1009694705 6.94E-06 NA mr1070 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
vg1009694705 4.21E-06 NA mr1070 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
vg1009694705 3.35E-06 NA mr1128 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
vg1009694705 3.30E-07 7.84E-07 mr1128 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
vg1009694705 9.05E-06 NA mr1147 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
vg1009694705 NA 7.77E-06 mr1437 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
vg1009694705 NA 2.08E-12 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
vg1009694705 NA 4.68E-10 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
vg1009694705 2.05E-06 NA mr1027_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
vg1009694705 NA 2.03E-09 mr1027_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
vg1009694705 5.83E-08 2.29E-10 mr1053_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
vg1009694705 1.23E-06 3.45E-07 mr1053_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
vg1009694705 NA 9.22E-07 mr1126_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
vg1009694705 3.92E-07 NA mr1128_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
vg1009694705 9.72E-06 NA mr1128_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
vg1009694705 9.87E-08 5.81E-14 mr1147_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
vg1009694705 5.29E-06 6.46E-06 mr1147_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
vg1009694705 9.99E-07 NA mr1204_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
vg1009694705 NA 4.87E-07 mr1250_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
vg1009694705 NA 1.33E-09 mr1649_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
vg1009694705 NA 1.79E-11 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
vg1009694705 NA 2.60E-10 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