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Detailed information for vg0610884530:

Variant ID: vg0610884530 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 10884530
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


CGTCACGTGAGATGAAGACTAAGTCAACCATGACACGTAGGCGCCACATCAGTGAAAACCACTCTCAAAACTACAGAGTCATTTTATACCGGTTTCGATA[G/A]
TTGGAGGAGTTGTGGTGTCGACGTTGAGGGAGGTGATTTAATCAAGAGCAAGAATTGAGGAATGTCAAATAGACTTATTCTGAGTAATAAGGTATAGTGG

Reverse complement sequence

CCACTATACCTTATTACTCAGAATAAGTCTATTTGACATTCCTCAATTCTTGCTCTTGATTAAATCACCTCCCTCAACGTCGACACCACAACTCCTCCAA[C/T]
TATCGAAACCGGTATAAAATGACTCTGTAGTTTTGAGAGTGGTTTTCACTGATGTGGCGCCTACGTGTCATGGTTGACTTAGTCTTCATCTCACGTGACG

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 86.30% 12.10% 0.04% 1.54% NA
All Indica  2759 77.10% 20.20% 0.07% 2.61% NA
All Japonica  1512 99.30% 0.60% 0.00% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 91.30% 8.60% 0.00% 0.17% NA
Indica II  465 84.70% 15.30% 0.00% 0.00% NA
Indica III  913 63.50% 29.90% 0.22% 6.35% NA
Indica Intermediate  786 77.60% 20.70% 0.00% 1.65% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.00% 0.20% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0610884530 G -> A LOC_Os06g19130.1 intron_variant ; MODIFIER silent_mutation Average:95.973; most accessible tissue: Zhenshan97 panicle, score: 98.467 N N N N
vg0610884530 G -> DEL N N silent_mutation Average:95.973; most accessible tissue: Zhenshan97 panicle, score: 98.467 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)
vg0610884530 G A 0.07 0.13 0.12 0.02 0.06 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0610884530 6.98E-06 NA mr1067 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
vg0610884530 7.00E-06 4.07E-07 mr1218 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
vg0610884530 8.23E-06 NA mr1221 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
vg0610884530 2.41E-06 1.07E-09 mr1221 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
vg0610884530 NA 1.63E-06 mr1242 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
vg0610884530 NA 7.27E-07 mr1422 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
vg0610884530 NA 7.05E-09 mr1583 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
vg0610884530 NA 6.75E-08 mr1124_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
vg0610884530 NA 1.45E-06 mr1632_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
vg0610884530 NA 1.52E-06 mr1946_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
vg0610884530 NA 1.52E-06 mr1948_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