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Detailed information for vg0104592595:

Variant ID: vg0104592595 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 4592595
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


CACAACAACAGTGCTAGTGCGATGCAGCGGCGGACTCGCACGCGGCGCGGAGTGGGCGTGGGTTGCGCGCGCGCGGGACGGCGGCGGCGCAACGCTATTG[C/T]
GTGATAAGATGAGATGAGATCGCATCGCTACGCTAGGGGCTAGGGCGAGAGGAGAGAGACAGAGTCGTGCAACGCCGCGACATTCTGAATTCGATACACG

Reverse complement sequence

CGTGTATCGAATTCAGAATGTCGCGGCGTTGCACGACTCTGTCTCTCTCCTCTCGCCCTAGCCCCTAGCGTAGCGATGCGATCTCATCTCATCTTATCAC[G/A]
CAATAGCGTTGCGCCGCCGCCGTCCCGCGCGCGCGCAACCCACGCCCACTCCGCGCCGCGTGCGAGTCCGCCGCTGCATCGCACTAGCACTGTTGTTGTG

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 61.70% 21.90% 0.51% 15.89% NA
All Indica  2759 82.10% 1.30% 0.11% 16.56% NA
All Japonica  1512 36.30% 62.50% 0.53% 0.66% NA
Aus  269 9.30% 0.70% 3.35% 86.62% NA
Indica I  595 69.40% 0.00% 0.17% 30.42% NA
Indica II  465 94.20% 3.20% 0.00% 2.58% NA
Indica III  913 80.40% 1.20% 0.00% 18.40% NA
Indica Intermediate  786 86.40% 1.10% 0.25% 12.21% NA
Temperate Japonica  767 59.60% 39.40% 0.26% 0.78% NA
Tropical Japonica  504 7.10% 91.50% 0.60% 0.79% NA
Japonica Intermediate  241 23.20% 75.50% 1.24% 0.00% NA
VI/Aromatic  96 27.10% 32.30% 0.00% 40.62% NA
Intermediate  90 56.70% 25.60% 4.44% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0104592595 C -> T LOC_Os01g09150.1 upstream_gene_variant ; 3465.0bp to feature; MODIFIER silent_mutation Average:73.119; most accessible tissue: Zhenshan97 panicle, score: 89.846 N N N N
vg0104592595 C -> T LOC_Os01g09130.1 downstream_gene_variant ; 4760.0bp to feature; MODIFIER silent_mutation Average:73.119; most accessible tissue: Zhenshan97 panicle, score: 89.846 N N N N
vg0104592595 C -> T LOC_Os01g09140.1 downstream_gene_variant ; 1223.0bp to feature; MODIFIER silent_mutation Average:73.119; most accessible tissue: Zhenshan97 panicle, score: 89.846 N N N N
vg0104592595 C -> T LOC_Os01g09140-LOC_Os01g09150 intergenic_region ; MODIFIER silent_mutation Average:73.119; most accessible tissue: Zhenshan97 panicle, score: 89.846 N N N N
vg0104592595 C -> DEL N N silent_mutation Average:73.119; most accessible tissue: Zhenshan97 panicle, score: 89.846 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)
vg0104592595 C T -0.09 -0.04 -0.05 -0.06 -0.1 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0104592595 NA 5.59E-07 mr1300 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
vg0104592595 NA 4.78E-07 mr1310 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
vg0104592595 NA 8.61E-07 mr1510 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
vg0104592595 NA 7.57E-09 mr1648 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
vg0104592595 NA 1.62E-06 mr1761 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
vg0104592595 NA 7.53E-14 mr1900 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
vg0104592595 NA 1.85E-12 mr1905 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
vg0104592595 NA 4.53E-08 mr1926 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
vg0104592595 NA 1.56E-07 mr1030_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
vg0104592595 NA 5.25E-07 mr1195_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
vg0104592595 NA 3.20E-08 mr1304_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
vg0104592595 NA 4.91E-08 mr1310_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
vg0104592595 NA 1.65E-06 mr1329_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
vg0104592595 NA 8.55E-06 mr1331_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
vg0104592595 NA 5.94E-06 mr1337_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
vg0104592595 NA 9.59E-08 mr1358_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
vg0104592595 NA 3.87E-06 mr1358_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
vg0104592595 NA 2.83E-11 mr1398_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
vg0104592595 NA 2.35E-06 mr1398_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
vg0104592595 NA 5.71E-06 mr1444_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
vg0104592595 NA 2.36E-06 mr1452_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
vg0104592595 8.09E-06 1.02E-25 mr1484_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
vg0104592595 NA 4.38E-06 mr1510_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
vg0104592595 NA 6.60E-07 mr1524_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
vg0104592595 NA 1.16E-13 mr1552_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
vg0104592595 NA 1.68E-07 mr1582_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
vg0104592595 1.22E-06 1.65E-16 mr1666_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
vg0104592595 NA 1.63E-07 mr1666_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
vg0104592595 NA 7.29E-11 mr1705_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
vg0104592595 NA 1.98E-06 mr1743_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
vg0104592595 NA 1.01E-09 mr1749_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
vg0104592595 NA 2.35E-16 mr1761_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
vg0104592595 NA 8.68E-07 mr1761_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
vg0104592595 NA 3.00E-07 mr1819_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
vg0104592595 NA 3.77E-09 mr1821_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
vg0104592595 NA 2.95E-20 mr1900_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
vg0104592595 NA 1.52E-08 mr1905_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
vg0104592595 2.88E-06 1.28E-21 mr1945_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
vg0104592595 NA 4.34E-07 mr1959_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