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Detailed information for vg0917838619:

Variant ID: vg0917838619 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 17838619
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTCGTCTGCTCATTTAACAGTCTCAGCGTGTCTGTCGAGTGAAGGAGACGAGAAATGCCTAGGGGTCTTCCGGCTAGCTCCACAAGGTGGTGGGCTAGA[C/T]
GACCTGGATTCAAAGCCTCACCCCTCCTAATTATTTGATATTAGGTCCTTCCCTAATATTCTAGTTTTTCGAGTGAAGGAGACTATGCCATGTTTGTTTT

Reverse complement sequence

AAAACAAACATGGCATAGTCTCCTTCACTCGAAAAACTAGAATATTAGGGAAGGACCTAATATCAAATAATTAGGAGGGGTGAGGCTTTGAATCCAGGTC[G/A]
TCTAGCCCACCACCTTGTGGAGCTAGCCGGAAGACCCCTAGGCATTTCTCGTCTCCTTCACTCGACAGACACGCTGAGACTGTTAAATGAGCAGACGAGT

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 76.60% 23.00% 0.42% 0.00% NA
All Indica  2759 97.50% 2.40% 0.11% 0.00% NA
All Japonica  1512 48.60% 50.50% 0.86% 0.00% NA
Aus  269 24.20% 75.80% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 98.10% 1.80% 0.11% 0.00% NA
Indica Intermediate  786 94.90% 4.80% 0.25% 0.00% NA
Temperate Japonica  767 73.90% 24.90% 1.17% 0.00% NA
Tropical Japonica  504 6.90% 92.70% 0.40% 0.00% NA
Japonica Intermediate  241 55.20% 44.00% 0.83% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 66.70% 28.90% 4.44% 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
vg0917838619 C -> T LOC_Os09g29370.1 upstream_gene_variant ; 3703.0bp to feature; MODIFIER silent_mutation Average:86.101; most accessible tissue: Zhenshan97 flower, score: 91.879 N N N N
vg0917838619 C -> T LOC_Os09g29390.1 upstream_gene_variant ; 4788.0bp to feature; MODIFIER silent_mutation Average:86.101; most accessible tissue: Zhenshan97 flower, score: 91.879 N N N N
vg0917838619 C -> T LOC_Os09g29380.1 downstream_gene_variant ; 591.0bp to feature; MODIFIER silent_mutation Average:86.101; most accessible tissue: Zhenshan97 flower, score: 91.879 N N N N
vg0917838619 C -> T LOC_Os09g29380.2 downstream_gene_variant ; 591.0bp to feature; MODIFIER silent_mutation Average:86.101; most accessible tissue: Zhenshan97 flower, score: 91.879 N N N N
vg0917838619 C -> T LOC_Os09g29380-LOC_Os09g29390 intergenic_region ; MODIFIER silent_mutation Average:86.101; most accessible tissue: Zhenshan97 flower, score: 91.879 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)
vg0917838619 C T 0.0 0.0 0.0 0.0 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0917838619 NA 1.52E-13 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0917838619 NA 7.52E-07 mr1031 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
vg0917838619 NA 1.73E-06 mr1252 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
vg0917838619 NA 4.32E-08 mr1354 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
vg0917838619 NA 5.56E-10 mr1379 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
vg0917838619 NA 4.20E-07 mr1554 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
vg0917838619 NA 5.52E-09 mr1559 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
vg0917838619 NA 2.20E-13 mr1578 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
vg0917838619 NA 4.73E-13 mr1696 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
vg0917838619 NA 2.46E-16 mr1819 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
vg0917838619 NA 2.84E-17 mr1916 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
vg0917838619 NA 5.72E-06 mr1092_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
vg0917838619 NA 7.59E-08 mr1097_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
vg0917838619 NA 6.35E-10 mr1220_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
vg0917838619 NA 1.90E-06 mr1263_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
vg0917838619 NA 4.63E-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
vg0917838619 NA 1.50E-08 mr1502_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
vg0917838619 NA 2.48E-18 mr1578_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
vg0917838619 NA 2.12E-14 mr1680_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
vg0917838619 NA 6.97E-06 mr1729_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
vg0917838619 NA 1.94E-13 mr1742_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
vg0917838619 NA 6.56E-10 mr1751_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
vg0917838619 NA 6.19E-15 mr1794_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
vg0917838619 NA 6.92E-10 mr1851_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