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Detailed information for vg1205512069:

Variant ID: vg1205512069 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 5512069
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.33, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


CTGAGCCGCCTTAAGTGCCACCTCGCCCCGTCCACCCCATTCTGAGCCGCCGCGTCCGGAGGAGGAGCAGAGGCATGGCGGCCGGAGGAGGGGGGGAGGC[G/A]
CGGCGGAGGAGAAGAGAAGGGGAGAGGGAGCCGACGGAGAGGCAGAGGAGCTCAGCACAAGGTCGAGCCAACGCCAATTCGGAGCCGGCGCTGTTGCCGC

Reverse complement sequence

GCGGCAACAGCGCCGGCTCCGAATTGGCGTTGGCTCGACCTTGTGCTGAGCTCCTCTGCCTCTCCGTCGGCTCCCTCTCCCCTTCTCTTCTCCTCCGCCG[C/T]
GCCTCCCCCCCTCCTCCGGCCGCCATGCCTCTGCTCCTCCTCCGGACGCGGCGGCTCAGAATGGGGTGGACGGGGCGAGGTGGCACTTAAGGCGGCTCAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.70% 42.70% 0.23% 2.37% NA
All Indica  2759 91.10% 7.40% 0.36% 1.16% NA
All Japonica  1512 1.50% 98.50% 0.00% 0.00% NA
Aus  269 7.10% 63.60% 0.37% 29.00% NA
Indica I  595 97.80% 2.00% 0.00% 0.17% NA
Indica II  465 92.30% 6.90% 0.65% 0.22% NA
Indica III  913 90.50% 7.10% 0.66% 1.75% NA
Indica Intermediate  786 86.10% 12.00% 0.13% 1.78% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 3.00% 97.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 97.90% 0.00% 1.04% NA
Intermediate  90 28.90% 70.00% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1205512069 G -> DEL N N silent_mutation Average:85.778; most accessible tissue: Zhenshan97 young leaf, score: 92.168 N N N N
vg1205512069 G -> A LOC_Os12g10410.1 intron_variant ; MODIFIER silent_mutation Average:85.778; most accessible tissue: Zhenshan97 young leaf, score: 92.168 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)
vg1205512069 G A -0.21 -0.14 -0.17 -0.17 -0.24 -0.24

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1205512069 NA 2.89E-27 mr1037 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
vg1205512069 NA 1.94E-47 mr1109 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
vg1205512069 NA 9.03E-16 mr1199 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
vg1205512069 NA 1.35E-30 mr1208 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
vg1205512069 NA 5.97E-14 mr1270 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
vg1205512069 NA 1.35E-08 mr1342 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
vg1205512069 NA 1.10E-12 mr1362 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
vg1205512069 NA 3.34E-42 mr1458 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
vg1205512069 NA 6.93E-26 mr1551 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
vg1205512069 NA 3.35E-19 mr1552 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
vg1205512069 NA 1.51E-08 mr1770 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
vg1205512069 NA 3.06E-32 mr1878 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
vg1205512069 4.00E-06 NA mr1912 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
vg1205512069 NA 7.53E-12 mr1914 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
vg1205512069 NA 6.92E-12 mr1938 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
vg1205512069 NA 2.00E-31 mr1037_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
vg1205512069 NA 3.24E-21 mr1164_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
vg1205512069 NA 1.43E-06 mr1363_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
vg1205512069 NA 6.86E-16 mr1457_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
vg1205512069 NA 1.40E-47 mr1458_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