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Detailed information for vg0608349804:

Variant ID: vg0608349804 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 8349804
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAGACACCCGTATCAAGCTAAACTCAATCCAAAATAGACTAAAATATGTTGGTGGAACCCCCTCAATTTCGTTCTAGCTCCGCCCTTGCTACCACCCCC[A/T]
AGACACACACAAGAATAATGCCCATGGTAGAGAGAGTGAGATGCGATGTAGAATTGGAGAACGTTGTGGTCAAGGATTAAGAGAGAAAGTTACTGATTAG

Reverse complement sequence

CTAATCAGTAACTTTCTCTCTTAATCCTTGACCACAACGTTCTCCAATTCTACATCGCATCTCACTCTCTCTACCATGGGCATTATTCTTGTGTGTGTCT[T/A]
GGGGGTGGTAGCAAGGGCGGAGCTAGAACGAAATTGAGGGGGTTCCACCAACATATTTTAGTCTATTTTGGATTGAGTTTAGCTTGATACGGGTGTCTAA

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 44.10% 30.60% 1.63% 23.68% NA
All Indica  2759 65.90% 2.00% 1.12% 31.03% NA
All Japonica  1512 14.70% 84.90% 0.26% 0.20% NA
Aus  269 1.10% 7.40% 0.37% 91.08% NA
Indica I  595 58.70% 0.50% 3.36% 37.48% NA
Indica II  465 91.80% 2.60% 0.22% 5.38% NA
Indica III  913 50.40% 2.10% 0.77% 46.77% NA
Indica Intermediate  786 73.90% 2.70% 0.38% 23.03% NA
Temperate Japonica  767 23.70% 76.10% 0.00% 0.13% NA
Tropical Japonica  504 1.20% 98.60% 0.00% 0.20% NA
Japonica Intermediate  241 14.10% 83.80% 1.66% 0.41% NA
VI/Aromatic  96 0.00% 54.20% 39.58% 6.25% NA
Intermediate  90 44.40% 42.20% 3.33% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0608349804 A -> T LOC_Os06g14750-LOC_Os06g14770 intergenic_region ; MODIFIER silent_mutation Average:72.636; most accessible tissue: Zhenshan97 root, score: 83.751 N N N N
vg0608349804 A -> DEL N N silent_mutation Average:72.636; most accessible tissue: Zhenshan97 root, score: 83.751 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)
vg0608349804 A T 0.01 0.02 0.01 0.02 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0608349804 NA 3.09E-14 mr1062 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
vg0608349804 NA 1.14E-08 mr1342 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
vg0608349804 NA 2.19E-06 mr1677 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
vg0608349804 NA 1.94E-21 mr1698 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
vg0608349804 NA 1.26E-36 mr1719 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
vg0608349804 NA 2.94E-15 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
vg0608349804 NA 1.23E-07 mr1030_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
vg0608349804 NA 2.80E-14 mr1035_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
vg0608349804 NA 2.69E-15 mr1162_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
vg0608349804 NA 1.03E-18 mr1342_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
vg0608349804 NA 3.20E-07 mr1408_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
vg0608349804 NA 3.18E-07 mr1482_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
vg0608349804 NA 6.26E-06 mr1524_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
vg0608349804 NA 4.15E-06 mr1555_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
vg0608349804 NA 1.50E-28 mr1617_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
vg0608349804 NA 1.83E-31 mr1631_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
vg0608349804 NA 7.81E-20 mr1637_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
vg0608349804 NA 9.72E-08 mr1748_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
vg0608349804 NA 3.53E-07 mr1754_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
vg0608349804 NA 1.07E-07 mr1783_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
vg0608349804 NA 5.87E-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
vg0608349804 NA 1.54E-07 mr1821_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