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Detailed information for vg1009502056:

Variant ID: vg1009502056 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9502056
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, T: 0.08, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


GCAGTCCTCTCCTCCTCTTCCTCCTCCCGCTTCTTCCTGCGCGCTGCCGTCATCGTGGTTGTCCTCCACCAGCTCGCTGCTTGGCCGCTGCCGTCTGCCG[A/T]
TGGACGTCGACTCTGACCCGGCCGCCAAGGGCAAGCCCACCCAGATAGACCTCGAGGACCAGGTACGCCGCAGCCGCTCGACTCGTCCCCACGGGAATTC

Reverse complement sequence

GAATTCCCGTGGGGACGAGTCGAGCGGCTGCGGCGTACCTGGTCCTCGAGGTCTATCTGGGTGGGCTTGCCCTTGGCGGCCGGGTCAGAGTCGACGTCCA[T/A]
CGGCAGACGGCAGCGGCCAAGCAGCGAGCTGGTGGAGGACAACCACGATGACGGCAGCGCGCAGGAAGAAGCGGGAGGAGGAAGAGGAGGAGAGGACTGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.90% 23.10% 0.78% 23.15% NA
All Indica  2759 43.20% 31.60% 0.87% 24.32% NA
All Japonica  1512 77.50% 1.20% 0.26% 21.03% NA
Aus  269 3.00% 61.30% 3.35% 32.34% NA
Indica I  595 26.70% 70.10% 0.67% 2.52% NA
Indica II  465 62.60% 17.00% 0.43% 20.00% NA
Indica III  913 40.30% 15.30% 0.77% 43.59% NA
Indica Intermediate  786 47.70% 29.90% 1.40% 20.99% NA
Temperate Japonica  767 83.80% 0.90% 0.39% 14.86% NA
Tropical Japonica  504 78.60% 0.80% 0.00% 20.63% NA
Japonica Intermediate  241 55.20% 2.90% 0.41% 41.49% NA
VI/Aromatic  96 69.80% 20.80% 0.00% 9.38% NA
Intermediate  90 67.80% 22.20% 0.00% 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
vg1009502056 A -> T LOC_Os10g18700.1 missense_variant ; p.Met87Leu; MODERATE nonsynonymous_codon ; M87L Average:41.354; most accessible tissue: Zhenshan97 flag leaf, score: 91.644 unknown unknown TOLERATED 0.63
vg1009502056 A -> DEL LOC_Os10g18700.1 N frameshift_variant Average:41.354; most accessible tissue: Zhenshan97 flag leaf, score: 91.644 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)
vg1009502056 A T 0.0 0.0 0.01 -0.02 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1009502056 NA 1.33E-06 mr1028 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
vg1009502056 2.32E-07 NA mr1053 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
vg1009502056 6.80E-07 4.03E-06 mr1053 Ind_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
vg1009502056 5.21E-06 2.67E-11 mr1128 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
vg1009502056 7.82E-07 2.19E-06 mr1128 Ind_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
vg1009502056 2.72E-06 NA mr1147 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
vg1009502056 3.75E-06 NA mr1147 Ind_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
vg1009502056 NA 4.37E-11 mr1307 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
vg1009502056 NA 4.65E-07 mr1369 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
vg1009502056 NA 2.47E-08 mr1442 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
vg1009502056 NA 8.41E-08 mr1453 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
vg1009502056 NA 2.80E-07 mr1652 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
vg1009502056 NA 7.02E-07 mr1662 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
vg1009502056 NA 2.26E-09 mr1730 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
vg1009502056 NA 1.82E-06 mr1027_2 Ind_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
vg1009502056 NA 6.90E-10 mr1161_2 Ind_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