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Detailed information for vg0206578247:

Variant ID: vg0206578247 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 6578247
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAAACTTTGCACCTAAGACCGTATATTTTCGCTATTTTGGGGTTCTATAGCTACTTTATTATGTTTCATTTTAGACTATGAAAAGTTAGGCTGCGTTCG[T/A]
TTGGAGAACAAAGGGAGTTTGTTGGAGTTTGTTTGTTTCGTTTTCCGCGCGCACGCTTCTCAAACTACTAAATAGTGTGTTTTTAGCAAAAATTTTCTAT

Reverse complement sequence

ATAGAAAATTTTTGCTAAAAACACACTATTTAGTAGTTTGAGAAGCGTGCGCGCGGAAAACGAAACAAACAAACTCCAACAAACTCCCTTTGTTCTCCAA[A/T]
CGAACGCAGCCTAACTTTTCATAGTCTAAAATGAAACATAATAAAGTAGCTATAGAACCCCAAAATAGCGAAAATATACGGTCTTAGGTGCAAAGTTTTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.90% 2.00% 0.47% 2.60% NA
All Indica  2759 99.80% 0.10% 0.04% 0.04% NA
All Japonica  1512 85.00% 5.80% 1.26% 8.00% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.00% 0.11% 0.11% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 94.70% 0.10% 0.65% 4.56% NA
Tropical Japonica  504 83.10% 12.70% 1.98% 2.18% NA
Japonica Intermediate  241 58.10% 9.10% 1.66% 31.12% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 4.40% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0206578247 T -> A LOC_Os02g12580.1 upstream_gene_variant ; 639.0bp to feature; MODIFIER silent_mutation Average:56.166; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0206578247 T -> A LOC_Os02g12590.1 upstream_gene_variant ; 712.0bp to feature; MODIFIER silent_mutation Average:56.166; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0206578247 T -> A LOC_Os02g12600.1 upstream_gene_variant ; 4081.0bp to feature; MODIFIER silent_mutation Average:56.166; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0206578247 T -> A LOC_Os02g12580-LOC_Os02g12590 intergenic_region ; MODIFIER silent_mutation Average:56.166; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0206578247 T -> DEL N N silent_mutation Average:56.166; most accessible tissue: Minghui63 panicle, score: 82.128 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)
vg0206578247 T A -0.02 -0.01 -0.01 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0206578247 NA 9.23E-06 mr1267_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
vg0206578247 8.01E-07 8.00E-07 mr1284_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
vg0206578247 2.63E-07 2.63E-07 mr1286_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
vg0206578247 3.19E-07 3.19E-07 mr1312_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
vg0206578247 1.23E-06 1.23E-06 mr1369_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
vg0206578247 5.29E-07 5.29E-07 mr1373_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
vg0206578247 2.38E-06 2.38E-06 mr1374_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
vg0206578247 7.66E-07 5.64E-08 mr1397_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
vg0206578247 1.57E-06 1.57E-06 mr1453_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
vg0206578247 NA 5.91E-06 mr1556_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
vg0206578247 4.12E-06 4.12E-06 mr1652_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
vg0206578247 6.70E-07 6.70E-07 mr1663_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
vg0206578247 7.31E-06 5.45E-07 mr1665_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
vg0206578247 2.22E-06 2.22E-06 mr1674_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
vg0206578247 9.65E-07 9.64E-07 mr1688_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
vg0206578247 7.78E-06 7.78E-06 mr1697_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
vg0206578247 NA 8.59E-07 mr1738_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
vg0206578247 NA 8.62E-07 mr1812_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
vg0206578247 2.58E-07 2.58E-07 mr1832_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
vg0206578247 NA 2.16E-06 mr1833_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
vg0206578247 9.97E-07 9.97E-07 mr1843_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
vg0206578247 1.80E-06 1.80E-06 mr1847_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