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Detailed information for vg1219159089:

Variant ID: vg1219159089 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19159089
Reference Allele: CAlternative Allele: G,T
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


AGAAGGAGGAGGAGAGGAGGAGGAAGGAGCGAGCGATGGCGTACCAGGAGCCCGAGTGGGCGAGGGTGGACGAGGATGAGGCGGCGGTGTTTGAGGACGA[C/G,T]
GAGGAGGAGGAGACGAGGGCGAAGAGGAAGGAGGAGCTGTACTGCGTGGCGTGTAATAAGAAGTTCAAGTCCGACAAGCAGTGGAAGAACCATGAGCAGT

Reverse complement sequence

ACTGCTCATGGTTCTTCCACTGCTTGTCGGACTTGAACTTCTTATTACACGCCACGCAGTACAGCTCCTCCTTCCTCTTCGCCCTCGTCTCCTCCTCCTC[G/C,A]
TCGTCCTCAAACACCGCCGCCTCATCCTCGTCCACCCTCGCCCACTCGGGCTCCTGGTACGCCATCGCTCGCTCCTTCCTCCTCCTCTCCTCCTCCTTCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.90% 46.00% 0.11% 0.00% T: 0.06%
All Indica  2759 78.50% 21.50% 0.07% 0.00% NA
All Japonica  1512 6.60% 93.10% 0.13% 0.00% T: 0.20%
Aus  269 89.60% 10.00% 0.37% 0.00% NA
Indica I  595 83.90% 16.10% 0.00% 0.00% NA
Indica II  465 91.80% 8.20% 0.00% 0.00% NA
Indica III  913 71.50% 28.40% 0.11% 0.00% NA
Indica Intermediate  786 74.60% 25.30% 0.13% 0.00% NA
Temperate Japonica  767 1.60% 97.90% 0.13% 0.00% T: 0.39%
Tropical Japonica  504 5.60% 94.40% 0.00% 0.00% NA
Japonica Intermediate  241 24.90% 74.70% 0.41% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 35.60% 64.40% 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
vg1219159089 C -> G LOC_Os12g31840.1 missense_variant ; p.Asp297Glu; MODERATE nonsynonymous_codon ; D297E Average:83.361; most accessible tissue: Minghui63 flag leaf, score: 93.46 unknown unknown TOLERATED 1.00
vg1219159089 C -> T LOC_Os12g31840.1 synonymous_variant ; p.Asp297Asp; LOW synonymous_codon Average:83.361; most accessible tissue: Minghui63 flag leaf, score: 93.46 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)
vg1219159089 C G 0.0 0.0 0.0 0.0 0.0 0.0
vg1219159089 C T 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219159089 NA 8.00E-06 mr1042 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
vg1219159089 NA 2.34E-06 mr1123 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
vg1219159089 NA 4.48E-06 mr1189 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
vg1219159089 4.71E-07 4.71E-07 mr1228 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
vg1219159089 5.50E-06 5.50E-06 mr1232 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
vg1219159089 NA 9.87E-06 mr1242 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
vg1219159089 NA 7.87E-06 mr1247 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
vg1219159089 8.63E-06 8.63E-06 mr1413 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
vg1219159089 NA 6.91E-06 mr1457 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
vg1219159089 NA 1.02E-11 mr1458 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
vg1219159089 3.04E-06 3.04E-06 mr1571 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
vg1219159089 7.08E-06 7.08E-06 mr1605 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
vg1219159089 NA 2.39E-06 mr1944 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
vg1219159089 NA 2.40E-07 mr1113_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
vg1219159089 NA 2.16E-07 mr1376_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
vg1219159089 NA 1.39E-07 mr1431_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
vg1219159089 NA 4.67E-12 mr1458_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
vg1219159089 NA 3.66E-06 mr1691_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