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Detailed information for vg0919909414:

Variant ID: vg0919909414 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19909414
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GCGTGTTCGATCCGTTCCTGCACCAGCAGACCAACAAAGCCCTTGTTCAATTCCTAACTTTTTCTTTAAACTTTCAACTTTTCCATCACATCAAAATTTT[C/T]
CTTCATACATAACTTCATACATAAACTTCTAGTTTTTTTCTTCAAACTTCCAATTTTAGTCAAACTTTTAATTTTAACGTGAAACTAAACACACGGAAAC

Reverse complement sequence

GTTTCCGTGTGTTTAGTTTCACGTTAAAATTAAAAGTTTGACTAAAATTGGAAGTTTGAAGAAAAAAACTAGAAGTTTATGTATGAAGTTATGTATGAAG[G/A]
AAAATTTTGATGTGATGGAAAAGTTGAAAGTTTAAAGAAAAAGTTAGGAATTGAACAAGGGCTTTGTTGGTCTGCTGGTGCAGGAACGGATCGAACACGC

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 98.20% 0.90% 0.89% 0.00% NA
All Indica  2759 98.00% 1.10% 0.87% 0.00% NA
All Japonica  1512 99.00% 0.20% 0.79% 0.00% NA
Aus  269 94.40% 3.30% 2.23% 0.00% NA
Indica I  595 96.50% 1.20% 2.35% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 98.40% 1.20% 0.44% 0.00% NA
Indica Intermediate  786 98.10% 1.30% 0.64% 0.00% NA
Temperate Japonica  767 98.00% 0.40% 1.56% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0919909414 C -> T LOC_Os09g33690.1 upstream_gene_variant ; 4862.0bp to feature; MODIFIER silent_mutation Average:84.899; most accessible tissue: Minghui63 root, score: 93.566 N N N N
vg0919909414 C -> T LOC_Os09g33700.1 upstream_gene_variant ; 1371.0bp to feature; MODIFIER silent_mutation Average:84.899; most accessible tissue: Minghui63 root, score: 93.566 N N N N
vg0919909414 C -> T LOC_Os09g33690.3 upstream_gene_variant ; 4940.0bp to feature; MODIFIER silent_mutation Average:84.899; most accessible tissue: Minghui63 root, score: 93.566 N N N N
vg0919909414 C -> T LOC_Os09g33690.2 upstream_gene_variant ; 4862.0bp to feature; MODIFIER silent_mutation Average:84.899; most accessible tissue: Minghui63 root, score: 93.566 N N N N
vg0919909414 C -> T LOC_Os09g33690.4 upstream_gene_variant ; 4862.0bp to feature; MODIFIER silent_mutation Average:84.899; most accessible tissue: Minghui63 root, score: 93.566 N N N N
vg0919909414 C -> T LOC_Os09g33710.1 intron_variant ; MODIFIER silent_mutation Average:84.899; most accessible tissue: Minghui63 root, score: 93.566 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)
vg0919909414 C T 0.0 0.0 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919909414 NA 2.73E-13 mr1069 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
vg0919909414 NA 1.80E-13 mr1149 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
vg0919909414 NA 7.83E-06 mr1231 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
vg0919909414 NA 9.41E-06 mr1531 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
vg0919909414 NA 1.75E-11 mr1557 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
vg0919909414 NA 1.89E-09 mr1598 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
vg0919909414 NA 1.64E-09 mr1660 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
vg0919909414 NA 4.35E-20 mr1817 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
vg0919909414 NA 4.29E-07 mr1137_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
vg0919909414 NA 2.96E-08 mr1174_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
vg0919909414 NA 5.98E-10 mr1232_2 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
vg0919909414 NA 4.96E-08 mr1299_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
vg0919909414 NA 3.79E-08 mr1347_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
vg0919909414 NA 3.28E-28 mr1441_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
vg0919909414 NA 1.68E-08 mr1482_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
vg0919909414 NA 2.87E-13 mr1557_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
vg0919909414 NA 4.82E-10 mr1565_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
vg0919909414 NA 3.40E-17 mr1592_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
vg0919909414 NA 7.23E-06 mr1592_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
vg0919909414 NA 1.18E-15 mr1598_2 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
vg0919909414 NA 4.11E-06 mr1617_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
vg0919909414 NA 5.93E-09 mr1962_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