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Detailed information for vg1218111047:

Variant ID: vg1218111047 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18111047
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


CACGCAAATCTAAAGTCATGTCATTTTAGTCATATGAATCAATTAGAAAAAAAAGAATCAATTGAAAAGACGACTGATTTCGCGCCTTATAATTGTTCAT[G/A]
GTATAGCTGGACATGACCCGGTCGTAGACTCGGTAGTACTCCCCAAGTGATATTAATTTATATGGCTCTCCCATGCTTGATCCCAGCATAAATTGCGCCC

Reverse complement sequence

GGGCGCAATTTATGCTGGGATCAAGCATGGGAGAGCCATATAAATTAATATCACTTGGGGAGTACTACCGAGTCTACGACCGGGTCATGTCCAGCTATAC[C/T]
ATGAACAATTATAAGGCGCGAAATCAGTCGTCTTTTCAATTGATTCTTTTTTTTCTAATTGATTCATATGACTAAAATGACATGACTTTAGATTTGCGTG

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 68.80% 30.90% 0.28% 0.08% NA
All Indica  2759 54.30% 45.20% 0.40% 0.14% NA
All Japonica  1512 87.70% 12.20% 0.07% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 19.80% 79.50% 0.50% 0.17% NA
Indica II  465 74.60% 24.90% 0.00% 0.43% NA
Indica III  913 63.70% 35.80% 0.44% 0.00% NA
Indica Intermediate  786 57.30% 42.10% 0.51% 0.13% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 76.00% 24.00% 0.00% 0.00% NA
Japonica Intermediate  241 74.70% 24.90% 0.41% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 81.10% 17.80% 1.11% 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
vg1218111047 G -> DEL N N silent_mutation Average:85.895; most accessible tissue: Minghui63 root, score: 98.781 N N N N
vg1218111047 G -> A LOC_Os12g30170.1 upstream_gene_variant ; 118.0bp to feature; MODIFIER silent_mutation Average:85.895; most accessible tissue: Minghui63 root, score: 98.781 N N N N
vg1218111047 G -> A LOC_Os12g30180.1 upstream_gene_variant ; 4861.0bp to feature; MODIFIER silent_mutation Average:85.895; most accessible tissue: Minghui63 root, score: 98.781 N N N N
vg1218111047 G -> A LOC_Os12g30160.1 downstream_gene_variant ; 1048.0bp to feature; MODIFIER silent_mutation Average:85.895; most accessible tissue: Minghui63 root, score: 98.781 N N N N
vg1218111047 G -> A LOC_Os12g30160-LOC_Os12g30170 intergenic_region ; MODIFIER silent_mutation Average:85.895; most accessible tissue: Minghui63 root, score: 98.781 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)
vg1218111047 G A 0.12 0.06 0.01 -0.01 0.05 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218111047 NA 1.40E-06 mr1139 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
vg1218111047 9.15E-06 NA mr1155 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
vg1218111047 NA 8.01E-07 mr1155 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
vg1218111047 NA 4.44E-06 mr1170 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
vg1218111047 NA 1.25E-08 mr1272 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
vg1218111047 NA 4.75E-06 mr1291 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
vg1218111047 NA 1.00E-06 mr1335 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
vg1218111047 NA 4.37E-08 mr1364 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
vg1218111047 NA 2.95E-08 mr1443 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
vg1218111047 NA 2.87E-06 mr1502 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
vg1218111047 8.72E-06 8.72E-06 mr1564 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
vg1218111047 NA 6.85E-06 mr1570 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
vg1218111047 NA 7.47E-10 mr1660 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
vg1218111047 NA 2.90E-08 mr1660 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
vg1218111047 NA 7.41E-06 mr1772 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
vg1218111047 NA 5.28E-06 mr1819 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
vg1218111047 NA 3.30E-08 mr1860 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
vg1218111047 NA 4.85E-06 mr1884 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
vg1218111047 NA 2.08E-06 mr1965 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
vg1218111047 NA 1.77E-07 mr1910_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