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Detailed information for vg1218339498:

Variant ID: vg1218339498 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 18339498
Reference Allele: GAlternative Allele: A,GTAA
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.76, G: 0.24, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


CATTTTTAGGTCCCTGAACTTGTCATGTGTGTCATATAGGTCCAAATGGGTTCTAACCTGCTCCATAGCGCTGACGTGGCAATGCCACGGTGACACCTAC[G/A,GTAA]
TGTCAGTGGAATCCACATGGCAAGCATATATAAAAAATAAAATTGAAAACCATATTTTCTCCTCTTAGATAGACAGAAAAAAAGATAAAAATTCTAAGGT

Reverse complement sequence

ACCTTAGAATTTTTATCTTTTTTTCTGTCTATCTAAGAGGAGAAAATATGGTTTTCAATTTTATTTTTTATATATGCTTGCCATGTGGATTCCACTGACA[C/T,TTAC]
GTAGGTGTCACCGTGGCATTGCCACGTCAGCGCTATGGAGCAGGTTAGAACCCATTTGGACCTATATGACACACATGACAAGTTCAGGGACCTAAAAATG

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 63.70% 36.10% 0.11% 0.00% GTAA: 0.04%
All Indica  2759 95.90% 4.00% 0.07% 0.00% GTAA: 0.07%
All Japonica  1512 7.30% 92.70% 0.07% 0.00% NA
Aus  269 71.40% 28.60% 0.00% 0.00% NA
Indica I  595 96.50% 3.20% 0.00% 0.00% GTAA: 0.34%
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 96.80% 3.10% 0.11% 0.00% NA
Indica Intermediate  786 93.50% 6.40% 0.13% 0.00% NA
Temperate Japonica  767 2.00% 98.00% 0.00% 0.00% NA
Tropical Japonica  504 5.20% 94.80% 0.00% 0.00% NA
Japonica Intermediate  241 28.60% 71.00% 0.41% 0.00% NA
VI/Aromatic  96 30.20% 69.80% 0.00% 0.00% NA
Intermediate  90 38.90% 58.90% 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
vg1218339498 G -> GTAA LOC_Os12g30540.1 intron_variant ; MODIFIER silent_mutation Average:75.697; most accessible tissue: Minghui63 root, score: 91.333 N N N N
vg1218339498 G -> A LOC_Os12g30540.1 intron_variant ; MODIFIER silent_mutation Average:75.697; most accessible tissue: Minghui63 root, score: 91.333 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)
vg1218339498 G A 0.0 0.0 -0.01 0.0 -0.01 0.0
vg1218339498 G GTAA 0.06 0.06 0.04 0.02 0.03 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218339498 NA 7.68E-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
vg1218339498 NA 1.34E-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
vg1218339498 NA 1.41E-46 mr1558 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
vg1218339498 4.15E-06 NA mr1693 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
vg1218339498 NA 4.02E-08 mr1693 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
vg1218339498 NA 3.18E-12 mr1940 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
vg1218339498 NA 5.17E-06 mr1242_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
vg1218339498 NA 1.08E-19 mr1362_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
vg1218339498 NA 2.47E-13 mr1496_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
vg1218339498 NA 1.11E-23 mr1708_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
vg1218339498 5.24E-08 2.86E-08 mr1750_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
vg1218339498 3.20E-07 3.20E-07 mr1987_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