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Detailed information for vg0903984505:

Variant ID: vg0903984505 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 3984505
Reference Allele: GAlternative Allele: A,T
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, T: 0.26, A: 0.09, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGATGATAGGATATTAGCAATAATTCTAGAAACAATTTGGAGAGATGAAAATTTGCCTATATCCTGTGGAGGGGTGGTCAGACCGCAGCCAGTAGGGT[G/A,T]
GTTAGACCGACATCATCAGGCCGGTCAGACCACCAGTGGTGGCCGGTTAGACTGACGGCATCAGGCCGGTCAGACCGCCCACCGGAGGCCAGTCAGACCG

Reverse complement sequence

CGGTCTGACTGGCCTCCGGTGGGCGGTCTGACCGGCCTGATGCCGTCAGTCTAACCGGCCACCACTGGTGGTCTGACCGGCCTGATGATGTCGGTCTAAC[C/T,A]
ACCCTACTGGCTGCGGTCTGACCACCCCTCCACAGGATATAGGCAAATTTTCATCTCTCCAAATTGTTTCTAGAATTATTGCTAATATCCTATCATCCTT

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 40.30% 33.50% 9.37% 15.23% T: 1.52%
All Indica  2759 57.30% 2.40% 14.82% 25.23% T: 0.25%
All Japonica  1512 0.70% 97.50% 0.00% 0.20% T: 1.59%
Aus  269 93.30% 0.00% 2.60% 3.72% T: 0.37%
Indica I  595 47.20% 4.70% 17.98% 29.41% T: 0.67%
Indica II  465 55.70% 1.30% 16.34% 26.67% NA
Indica III  913 61.80% 0.80% 12.92% 24.42% T: 0.11%
Indica Intermediate  786 60.80% 3.10% 13.74% 22.14% T: 0.25%
Temperate Japonica  767 0.50% 98.70% 0.00% 0.13% T: 0.65%
Tropical Japonica  504 0.80% 96.80% 0.00% 0.20% T: 2.18%
Japonica Intermediate  241 1.20% 95.00% 0.00% 0.41% T: 3.32%
VI/Aromatic  96 35.40% 8.30% 19.79% 1.04% T: 35.42%
Intermediate  90 31.10% 42.20% 8.89% 11.11% T: 6.67%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0903984505 G -> DEL N N silent_mutation Average:73.151; most accessible tissue: Zhenshan97 flag leaf, score: 86.452 N N N N
vg0903984505 G -> T LOC_Os09g07840.1 downstream_gene_variant ; 4402.0bp to feature; MODIFIER silent_mutation Average:73.151; most accessible tissue: Zhenshan97 flag leaf, score: 86.452 N N N N
vg0903984505 G -> T LOC_Os09g07850.1 intron_variant ; MODIFIER silent_mutation Average:73.151; most accessible tissue: Zhenshan97 flag leaf, score: 86.452 N N N N
vg0903984505 G -> A LOC_Os09g07840.1 downstream_gene_variant ; 4402.0bp to feature; MODIFIER silent_mutation Average:73.151; most accessible tissue: Zhenshan97 flag leaf, score: 86.452 N N N N
vg0903984505 G -> A LOC_Os09g07850.1 intron_variant ; MODIFIER silent_mutation Average:73.151; most accessible tissue: Zhenshan97 flag leaf, score: 86.452 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)
vg0903984505 G A -0.01 -0.01 -0.01 -0.01 -0.01 -0.01
vg0903984505 G T -0.02 -0.02 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0903984505 NA 5.63E-100 mr1009 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
vg0903984505 NA 1.20E-20 mr1102 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
vg0903984505 NA 7.71E-23 mr1122 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
vg0903984505 NA 9.72E-22 mr1168 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
vg0903984505 NA 1.99E-09 mr1191 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
vg0903984505 NA 3.95E-45 mr1194 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
vg0903984505 NA 2.92E-15 mr1276 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
vg0903984505 NA 2.77E-23 mr1383 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
vg0903984505 NA 7.28E-39 mr1480 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
vg0903984505 NA 6.91E-09 mr1644 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
vg0903984505 NA 2.11E-08 mr1806 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
vg0903984505 NA 1.04E-23 mr1917 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
vg0903984505 NA 8.40E-34 mr1932 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
vg0903984505 NA 4.69E-20 mr1010_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
vg0903984505 NA 1.91E-34 mr1102_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
vg0903984505 NA 9.74E-23 mr1168_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
vg0903984505 NA 5.24E-56 mr1194_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
vg0903984505 NA 1.10E-37 mr1223_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
vg0903984505 NA 1.03E-51 mr1261_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
vg0903984505 NA 7.55E-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
vg0903984505 NA 6.09E-21 mr1298_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
vg0903984505 NA 1.72E-14 mr1529_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
vg0903984505 NA 2.28E-08 mr1576_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
vg0903984505 NA 2.97E-08 mr1659_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
vg0903984505 NA 2.05E-08 mr1660_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
vg0903984505 NA 2.27E-11 mr1714_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
vg0903984505 NA 9.41E-13 mr1717_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
vg0903984505 NA 2.16E-18 mr1730_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
vg0903984505 NA 4.48E-20 mr1731_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
vg0903984505 NA 8.94E-12 mr1781_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
vg0903984505 NA 7.22E-10 mr1806_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
vg0903984505 NA 6.78E-19 mr1817_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
vg0903984505 NA 9.44E-17 mr1866_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