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Detailed information for vg0709963229:

Variant ID: vg0709963229 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9963229
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTAGGTTGTTTTTTTTTAACGGAGGGAATACTCATCATATTATATGATTTTTTAGCTAAGGACGCAGTATTAAATTCATTGACATTGAGAGTGTGCTC[C/T]
GGATGCCACTATATATAAATATATAAATAGACAGAGGGAGGGACAGGGAGAGAGAATGGGTATCTCAAATGCTCTGCAATGGTGGGAGGAGTGGCAGCTC

Reverse complement sequence

GAGCTGCCACTCCTCCCACCATTGCAGAGCATTTGAGATACCCATTCTCTCTCCCTGTCCCTCCCTCTGTCTATTTATATATTTATATATAGTGGCATCC[G/A]
GAGCACACTCTCAATGTCAATGAATTTAATACTGCGTCCTTAGCTAAAAAATCATATAATATGATGAGTATTCCCTCCGTTAAAAAAAAACAACCTAAAT

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 74.90% 10.60% 1.40% 13.08% NA
All Indica  2759 81.90% 7.10% 0.36% 10.62% NA
All Japonica  1512 64.00% 12.50% 2.84% 20.63% NA
Aus  269 74.70% 23.40% 1.86% 0.00% NA
Indica I  595 69.20% 0.50% 0.00% 30.25% NA
Indica II  465 94.20% 0.40% 0.43% 4.95% NA
Indica III  913 89.70% 9.50% 0.44% 0.33% NA
Indica Intermediate  786 75.30% 13.10% 0.51% 11.07% NA
Temperate Japonica  767 59.30% 8.10% 2.35% 30.25% NA
Tropical Japonica  504 83.30% 14.10% 1.59% 0.99% NA
Japonica Intermediate  241 38.60% 23.20% 7.05% 31.12% NA
VI/Aromatic  96 37.50% 43.80% 8.33% 10.42% NA
Intermediate  90 82.20% 14.40% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0709963229 C -> DEL N N silent_mutation Average:73.013; most accessible tissue: Callus, score: 87.227 N N N N
vg0709963229 C -> T LOC_Os07g16930.1 upstream_gene_variant ; 56.0bp to feature; MODIFIER silent_mutation Average:73.013; most accessible tissue: Callus, score: 87.227 N N N N
vg0709963229 C -> T LOC_Os07g16920-LOC_Os07g16930 intergenic_region ; MODIFIER silent_mutation Average:73.013; most accessible tissue: Callus, score: 87.227 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)
vg0709963229 C T 0.03 -0.02 -0.01 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709963229 NA 3.31E-06 mr1028 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
vg0709963229 2.86E-06 NA mr1117 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
vg0709963229 5.04E-06 NA mr1117 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
vg0709963229 5.39E-07 NA mr1119 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
vg0709963229 NA 1.55E-06 mr1280 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
vg0709963229 4.98E-06 NA mr1496 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
vg0709963229 NA 2.79E-06 mr1510 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
vg0709963229 NA 1.59E-06 mr1652 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
vg0709963229 NA 9.12E-07 mr1788 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
vg0709963229 4.28E-06 NA mr1114_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
vg0709963229 5.68E-06 NA 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
vg0709963229 1.61E-06 NA mr1117_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
vg0709963229 7.43E-06 NA 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
vg0709963229 3.56E-06 NA 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
vg0709963229 4.12E-06 NA mr1119_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
vg0709963229 1.30E-06 NA mr1120_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
vg0709963229 NA 1.08E-06 mr1458_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
vg0709963229 3.09E-06 NA mr1496_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
vg0709963229 5.16E-06 NA 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
vg0709963229 NA 3.45E-06 mr1788_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