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Detailed information for vg1128827572:

Variant ID: vg1128827572 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28827572
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTGTAGCCATAGTAAATCCAATAACACTCGCCATCAATATGGAGACTAAAATTTGTGAGAAACCAAAATCAAAATCAAAATCAAATGCTCTACAAAAA[G/A]
CTTCACTGTCAAATAATGGCCATTGGACGAGAGATAACTTGTATTGACTAATTCCAGACAGCCTAATAGCCTATATCATTGGGACACGTAGCAACGCCGT

Reverse complement sequence

ACGGCGTTGCTACGTGTCCCAATGATATAGGCTATTAGGCTGTCTGGAATTAGTCAATACAAGTTATCTCTCGTCCAATGGCCATTATTTGACAGTGAAG[C/T]
TTTTTGTAGAGCATTTGATTTTGATTTTGATTTTGGTTTCTCACAAATTTTAGTCTCCATATTGATGGCGAGTGTTATTGGATTTACTATGGCTACAACT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.80% 11.10% 0.11% 0.00% NA
All Indica  2759 88.40% 11.40% 0.18% 0.00% NA
All Japonica  1512 93.70% 6.30% 0.00% 0.00% NA
Aus  269 68.40% 31.60% 0.00% 0.00% NA
Indica I  595 89.40% 10.30% 0.34% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 83.60% 16.40% 0.00% 0.00% NA
Indica Intermediate  786 87.20% 12.50% 0.38% 0.00% NA
Temperate Japonica  767 92.30% 7.70% 0.00% 0.00% NA
Tropical Japonica  504 95.80% 4.20% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1128827572 G -> A LOC_Os11g47809.1 upstream_gene_variant ; 104.0bp to feature; MODIFIER silent_mutation Average:90.198; most accessible tissue: Zhenshan97 flag leaf, score: 98.685 N N N N
vg1128827572 G -> A LOC_Os11g47800.1 downstream_gene_variant ; 3327.0bp to feature; MODIFIER silent_mutation Average:90.198; most accessible tissue: Zhenshan97 flag leaf, score: 98.685 N N N N
vg1128827572 G -> A LOC_Os11g47800-LOC_Os11g47809 intergenic_region ; MODIFIER silent_mutation Average:90.198; most accessible tissue: Zhenshan97 flag leaf, score: 98.685 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)
vg1128827572 G A -0.02 -0.03 -0.01 -0.03 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128827572 NA 9.83E-06 mr1860 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
vg1128827572 NA 7.02E-06 mr1549_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
vg1128827572 NA 4.62E-06 mr1655_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
vg1128827572 NA 7.68E-06 mr1669_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
vg1128827572 7.67E-07 4.64E-07 mr1757_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
vg1128827572 NA 2.24E-06 mr1977_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