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Detailed information for vg0114895999:

Variant ID: vg0114895999 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14895999
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GCATCTGCCCGCCACTATTCTCGAGTCCCCCTCCGCCGCCCTAACTACCTCCACCCTTGCCGATGACGGCAACTCTCCCTCCGCTGTCCCGACTACCTGC[A/G]
TCCATAGTGGAAAAAACCGGACCGGTAGATGACCCGGTCACCCTGCTGGTTCACCAGTTTGACGGTCCAATTGTGAAGCGGCCGGTCAAACCGCGGTTCA

Reverse complement sequence

TGAACCGCGGTTTGACCGGCCGCTTCACAATTGGACCGTCAAACTGGTGAACCAGCAGGGTGACCGGGTCATCTACCGGTCCGGTTTTTTCCACTATGGA[T/C]
GCAGGTAGTCGGGACAGCGGAGGGAGAGTTGCCGTCATCGGCAAGGGTGGAGGTAGTTAGGGCGGCGGAGGGGGACTCGAGAATAGTGGCGGGCAGATGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.70% 36.20% 0.23% 15.83% NA
All Indica  2759 73.70% 8.10% 0.22% 18.01% NA
All Japonica  1512 0.40% 87.10% 0.07% 12.43% NA
Aus  269 45.70% 33.10% 0.74% 20.45% NA
Indica I  595 64.40% 18.20% 0.17% 17.31% NA
Indica II  465 82.40% 5.20% 0.43% 12.04% NA
Indica III  913 72.20% 2.40% 0.11% 25.30% NA
Indica Intermediate  786 77.40% 8.80% 0.25% 13.61% NA
Temperate Japonica  767 0.10% 94.50% 0.00% 5.35% NA
Tropical Japonica  504 0.20% 91.50% 0.20% 8.13% NA
Japonica Intermediate  241 1.70% 54.40% 0.00% 43.98% NA
VI/Aromatic  96 58.30% 39.60% 1.04% 1.04% NA
Intermediate  90 42.20% 48.90% 1.11% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0114895999 A -> G LOC_Os01g26280.1 upstream_gene_variant ; 686.0bp to feature; MODIFIER silent_mutation Average:51.293; most accessible tissue: Zhenshan97 young leaf, score: 88.878 N N N N
vg0114895999 A -> G LOC_Os01g26270.1 downstream_gene_variant ; 2056.0bp to feature; MODIFIER silent_mutation Average:51.293; most accessible tissue: Zhenshan97 young leaf, score: 88.878 N N N N
vg0114895999 A -> G LOC_Os01g26270-LOC_Os01g26280 intergenic_region ; MODIFIER silent_mutation Average:51.293; most accessible tissue: Zhenshan97 young leaf, score: 88.878 N N N N
vg0114895999 A -> DEL N N silent_mutation Average:51.293; most accessible tissue: Zhenshan97 young leaf, score: 88.878 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)
vg0114895999 A G -0.06 -0.03 -0.06 -0.05 -0.06 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0114895999 NA 3.69E-06 mr1064 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
vg0114895999 NA 9.02E-06 mr1123 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
vg0114895999 NA 1.49E-06 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
vg0114895999 NA 5.45E-07 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
vg0114895999 4.18E-09 7.38E-10 mr1719 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
vg0114895999 6.15E-06 6.15E-06 mr1891 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
vg0114895999 NA 5.44E-06 mr1020_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
vg0114895999 NA 9.85E-09 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
vg0114895999 NA 5.85E-06 mr1118_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
vg0114895999 NA 4.17E-06 mr1119_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
vg0114895999 NA 1.55E-09 mr1198_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
vg0114895999 NA 1.00E-07 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
vg0114895999 NA 7.30E-06 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
vg0114895999 NA 2.14E-07 mr1275_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
vg0114895999 NA 7.74E-06 mr1405_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
vg0114895999 NA 1.55E-07 mr1496_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
vg0114895999 NA 3.34E-06 mr1519_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
vg0114895999 NA 4.53E-06 mr1745_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
vg0114895999 NA 2.06E-09 mr1835_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
vg0114895999 NA 6.48E-08 mr1909_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