Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1020839196:

Variant ID: vg1020839196 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 20839196
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTACGGCGGTAACTGCTAGGGGAAAAACGACTCGTTTAGTTTATTTTTTTAGGTAAAAAAGGTTGTAATAGTGTGTTTTAAGTTTTAACCGTGTGGGCTT[G/T]
CGCATGGGGAACGTGGTCGAAAATTCCGACGTAGTTGGACCCGAGCCGGACTCGAGGGAGACCGGCAGGTGAGAAAGGTGAAAGAAAAGGGGAAAGGTGA

Reverse complement sequence

TCACCTTTCCCCTTTTCTTTCACCTTTCTCACCTGCCGGTCTCCCTCGAGTCCGGCTCGGGTCCAACTACGTCGGAATTTTCGACCACGTTCCCCATGCG[C/A]
AAGCCCACACGGTTAAAACTTAAAACACACTATTACAACCTTTTTTACCTAAAAAAATAAACTAAACGAGTCGTTTTTCCCCTAGCAGTTACCGCCGTAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.70% 35.10% 0.04% 0.23% NA
All Indica  2759 98.80% 0.80% 0.04% 0.29% NA
All Japonica  1512 3.40% 96.30% 0.07% 0.20% NA
Aus  269 56.50% 43.50% 0.00% 0.00% NA
Indica I  595 99.20% 0.20% 0.17% 0.50% NA
Indica II  465 98.90% 0.90% 0.00% 0.22% NA
Indica III  913 99.60% 0.30% 0.00% 0.11% NA
Indica Intermediate  786 97.70% 1.90% 0.00% 0.38% NA
Temperate Japonica  767 1.70% 98.20% 0.00% 0.13% NA
Tropical Japonica  504 4.80% 94.80% 0.00% 0.40% NA
Japonica Intermediate  241 6.20% 93.40% 0.41% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg1020839196 G -> T LOC_Os10g39090.1 upstream_gene_variant ; 181.0bp to feature; MODIFIER silent_mutation Average:78.518; most accessible tissue: Zhenshan97 flag leaf, score: 99.553 N N N N
vg1020839196 G -> T LOC_Os10g39100.1 upstream_gene_variant ; 3640.0bp to feature; MODIFIER silent_mutation Average:78.518; most accessible tissue: Zhenshan97 flag leaf, score: 99.553 N N N N
vg1020839196 G -> T LOC_Os10g39090.2 upstream_gene_variant ; 172.0bp to feature; MODIFIER silent_mutation Average:78.518; most accessible tissue: Zhenshan97 flag leaf, score: 99.553 N N N N
vg1020839196 G -> T LOC_Os10g39090-LOC_Os10g39100 intergenic_region ; MODIFIER silent_mutation Average:78.518; most accessible tissue: Zhenshan97 flag leaf, score: 99.553 N N N N
vg1020839196 G -> DEL N N silent_mutation Average:78.518; most accessible tissue: Zhenshan97 flag leaf, score: 99.553 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)
vg1020839196 G T -0.07 -0.04 -0.03 -0.03 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1020839196 1.59E-06 NA mr1013 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
vg1020839196 NA 5.08E-21 mr1021 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
vg1020839196 1.21E-06 NA mr1031 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
vg1020839196 8.44E-07 NA mr1056 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
vg1020839196 NA 3.91E-22 mr1477 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
vg1020839196 NA 3.57E-47 mr1509 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
vg1020839196 1.87E-06 2.42E-62 mr1558 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
vg1020839196 NA 3.51E-09 mr1578 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
vg1020839196 NA 4.51E-10 mr1714 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
vg1020839196 NA 1.03E-12 mr1744 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
vg1020839196 NA 1.05E-29 mr1793 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
vg1020839196 NA 7.78E-11 mr1819 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
vg1020839196 NA 8.99E-36 mr1828 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
vg1020839196 NA 4.95E-18 mr1913 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
vg1020839196 NA 1.25E-11 mr1938 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
vg1020839196 NA 6.18E-16 mr1950 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
vg1020839196 NA 6.55E-19 mr1167_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
vg1020839196 NA 1.59E-08 mr1172_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
vg1020839196 NA 1.51E-25 mr1323_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
vg1020839196 NA 7.15E-30 mr1477_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
vg1020839196 NA 7.37E-50 mr1509_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
vg1020839196 2.81E-06 5.89E-78 mr1558_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
vg1020839196 NA 3.55E-17 mr1578_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
vg1020839196 NA 4.76E-21 mr1581_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
vg1020839196 NA 1.13E-22 mr1698_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
vg1020839196 NA 1.40E-18 mr1746_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
vg1020839196 NA 1.45E-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
vg1020839196 NA 7.28E-33 mr1913_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
vg1020839196 NA 7.07E-15 mr1950_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