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Detailed information for vg1123611068:

Variant ID: vg1123611068 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23611068
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, C: 0.39, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


CCATCGCCGTCTCCTCCTCTTCTCCGGCGTCCAAGAACCCCTCCCGTGCCCCGGCCATGCCGCCGCCGGAGCCGGACAAGGACAAGCCGCTGCCGAAGCC[C/G]
AAGCCGCCCAAGCCCAAGCCCAAGCCGCCCAAGCCGGAGCCGGAGCCGAACACGCGCTCGGCGCCGGAGCGCGACCAGACGGCCGCCCCGTACGGCACGG

Reverse complement sequence

CCGTGCCGTACGGGGCGGCCGTCTGGTCGCGCTCCGGCGCCGAGCGCGTGTTCGGCTCCGGCTCCGGCTTGGGCGGCTTGGGCTTGGGCTTGGGCGGCTT[G/C]
GGCTTCGGCAGCGGCTTGTCCTTGTCCGGCTCCGGCGGCGGCATGGCCGGGGCACGGGAGGGGTTCTTGGACGCCGGAGAAGAGGAGGAGACGGCGATGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.00% 33.10% 4.08% 1.90% NA
All Indica  2759 56.70% 34.10% 6.23% 2.90% NA
All Japonica  1512 67.40% 32.30% 0.26% 0.00% NA
Aus  269 72.90% 18.20% 5.20% 3.72% NA
Indica I  595 37.80% 49.90% 11.09% 1.18% NA
Indica II  465 29.90% 68.40% 0.86% 0.86% NA
Indica III  913 79.40% 8.50% 5.91% 6.13% NA
Indica Intermediate  786 60.60% 31.70% 6.11% 1.65% NA
Temperate Japonica  767 68.10% 31.80% 0.13% 0.00% NA
Tropical Japonica  504 58.10% 41.90% 0.00% 0.00% NA
Japonica Intermediate  241 84.60% 14.10% 1.24% 0.00% NA
VI/Aromatic  96 61.50% 37.50% 1.04% 0.00% NA
Intermediate  90 46.70% 51.10% 2.22% 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
vg1123611068 C -> DEL LOC_Os11g39640.1 N frameshift_variant Average:98.335; most accessible tissue: Minghui63 flag leaf, score: 99.689 N N N N
vg1123611068 C -> G LOC_Os11g39640.1 synonymous_variant ; p.Pro15Pro; LOW synonymous_codon Average:98.335; most accessible tissue: Minghui63 flag leaf, score: 99.689 N N N N
vg1123611068 C -> G LOC_Os11g39640.1 synonymous_variant ; p.Pro15Pro; LOW nonsynonymous_codon ; P15L Average:98.335; most accessible tissue: Minghui63 flag leaf, score: 99.689 unknown unknown DELETERIOUS 0.00

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)
vg1123611068 C G -0.04 -0.05 -0.01 -0.05 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123611068 1.76E-07 6.45E-16 mr1133 Ind_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
vg1123611068 8.30E-06 7.93E-10 mr1667 Ind_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
vg1123611068 NA 5.02E-09 mr1133_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
vg1123611068 NA 1.68E-06 mr1380_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
vg1123611068 NA 1.02E-06 mr1540_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
vg1123611068 NA 3.59E-07 mr1561_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
vg1123611068 NA 2.14E-07 mr1667_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
vg1123611068 NA 1.21E-06 mr1732_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
vg1123611068 NA 9.22E-08 mr1875_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
vg1123611068 NA 5.35E-07 mr1908_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