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Detailed information for vg0424049928:

Variant ID: vg0424049928 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 24049928
Reference Allele: AAlternative Allele: G,ATAG
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


CGGCGATGAACATGTCCTGCAAGACCACACATTTCGGTTTCGATCGATCAAAATGTCCAGGAAAACGGGGAAGCACCAGCGGTGTGGTGGTTGAGTCGTG[A/G,ATAG]
GTACATGACTCCAGTCTATCCACTAAAGTTTAAATTCTGATGCTCAAATTTTACACGCACACAGAGCTTTCGACCGACCGAAATTTAGTGAGATAAGAAA

Reverse complement sequence

TTTCTTATCTCACTAAATTTCGGTCGGTCGAAAGCTCTGTGTGCGTGTAAAATTTGAGCATCAGAATTTAAACTTTAGTGGATAGACTGGAGTCATGTAC[T/C,CTAT]
CACGACTCAACCACCACACCGCTGGTGCTTCCCCGTTTTCCTGGACATTTTGATCGATCGAAACCGAAATGTGTGGTCTTGCAGGACATGTTCATCGCCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.10% 3.10% 0.76% 0.00% ATAG: 0.02%
All Indica  2759 99.70% 0.20% 0.14% 0.00% NA
All Japonica  1512 88.90% 9.10% 2.05% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.40% 0.38% 0.00% NA
Temperate Japonica  767 96.60% 1.30% 2.09% 0.00% NA
Tropical Japonica  504 88.30% 11.10% 0.60% 0.00% NA
Japonica Intermediate  241 65.60% 29.50% 4.98% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 1.11% 0.00% ATAG: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0424049928 A -> G LOC_Os04g40460.1 upstream_gene_variant ; 2874.0bp to feature; MODIFIER silent_mutation Average:83.067; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0424049928 A -> G LOC_Os04g40490.1 upstream_gene_variant ; 4957.0bp to feature; MODIFIER silent_mutation Average:83.067; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0424049928 A -> G LOC_Os04g40475.1 downstream_gene_variant ; 3019.0bp to feature; MODIFIER silent_mutation Average:83.067; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0424049928 A -> G LOC_Os04g40470.1 intron_variant ; MODIFIER silent_mutation Average:83.067; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0424049928 A -> ATAG LOC_Os04g40460.1 upstream_gene_variant ; 2875.0bp to feature; MODIFIER silent_mutation Average:83.067; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0424049928 A -> ATAG LOC_Os04g40490.1 upstream_gene_variant ; 4956.0bp to feature; MODIFIER silent_mutation Average:83.067; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0424049928 A -> ATAG LOC_Os04g40475.1 downstream_gene_variant ; 3018.0bp to feature; MODIFIER silent_mutation Average:83.067; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0424049928 A -> ATAG LOC_Os04g40470.1 intron_variant ; MODIFIER silent_mutation Average:83.067; most accessible tissue: Minghui63 flower, score: 93.128 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)
vg0424049928 A ATAG -0.09 0.08 0.14 0.0 0.02 -0.15
vg0424049928 A G -0.01 0.01 0.02 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0424049928 NA 1.56E-06 mr1113 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
vg0424049928 7.50E-06 3.18E-08 mr1114 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
vg0424049928 NA 7.89E-06 mr1116 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
vg0424049928 2.47E-07 5.16E-11 mr1117 Jap_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
vg0424049928 NA 2.28E-09 mr1118 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
vg0424049928 2.06E-06 1.10E-08 mr1119 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
vg0424049928 NA 5.52E-07 mr1120 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
vg0424049928 1.57E-07 1.85E-11 mr1123 Jap_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
vg0424049928 NA 3.58E-08 mr1240 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
vg0424049928 3.41E-06 1.81E-10 mr1242 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
vg0424049928 1.63E-06 4.83E-09 mr1247 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
vg0424049928 NA 1.18E-06 mr1495 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
vg0424049928 5.53E-07 1.09E-10 mr1496 Jap_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
vg0424049928 NA 6.40E-06 mr1691 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
vg0424049928 NA 3.99E-09 mr1693 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
vg0424049928 NA 5.03E-06 mr1917 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
vg0424049928 NA 1.90E-06 mr1936 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
vg0424049928 1.37E-06 2.07E-08 mr1961 Jap_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
vg0424049928 5.24E-06 1.82E-08 mr1113_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
vg0424049928 1.42E-06 1.47E-09 mr1114_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
vg0424049928 1.16E-07 1.26E-11 mr1117_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
vg0424049928 1.43E-07 1.18E-11 mr1118_2 Jap_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
vg0424049928 1.76E-07 4.31E-11 mr1119_2 Jap_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
vg0424049928 8.82E-07 1.16E-09 mr1120_2 Jap_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
vg0424049928 1.51E-07 3.41E-11 mr1123_2 Jap_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
vg0424049928 2.07E-07 1.03E-11 mr1240_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
vg0424049928 5.80E-06 6.14E-10 mr1242_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
vg0424049928 9.68E-07 1.05E-09 mr1247_2 Jap_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
vg0424049928 NA 8.36E-09 mr1495_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
vg0424049928 1.58E-08 1.67E-13 mr1496_2 Jap_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
vg0424049928 NA 5.07E-08 mr1936_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
vg0424049928 1.91E-07 2.92E-09 mr1961_2 Jap_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