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Detailed information for vg0616706040:

Variant ID: vg0616706040 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 16706040
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAAAACGATTCGATTGATTGATTGTAGATTGGTTTTTTACAATGAACCGGCCATGTCCCTTATATAGGGGTTGGTCTTGCCCTCTACAGGCCCTCCTCT[A/G]
CGTTCAACTCGGGGTAGAAACTAAAGGAAACCCGAAACATGCTTTCCCGAGCAAGGAAACCTCGAGACCCGACGAAACACAGTCGGACTCGGACCTGCCG

Reverse complement sequence

CGGCAGGTCCGAGTCCGACTGTGTTTCGTCGGGTCTCGAGGTTTCCTTGCTCGGGAAAGCATGTTTCGGGTTTCCTTTAGTTTCTACCCCGAGTTGAACG[T/C]
AGAGGAGGGCCTGTAGAGGGCAAGACCAACCCCTATATAAGGGACATGGCCGGTTCATTGTAAAAAACCAATCTACAATCAATCAATCGAATCGTTTTTC

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 95.80% 4.20% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 32.00% 68.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0616706040 A -> G LOC_Os06g29270.1 downstream_gene_variant ; 361.0bp to feature; MODIFIER silent_mutation Average:65.693; most accessible tissue: Zhenshan97 young leaf, score: 87.443 N N N N
vg0616706040 A -> G LOC_Os06g29260.2 downstream_gene_variant ; 3657.0bp to feature; MODIFIER silent_mutation Average:65.693; most accessible tissue: Zhenshan97 young leaf, score: 87.443 N N N N
vg0616706040 A -> G LOC_Os06g29260.4 downstream_gene_variant ; 3621.0bp to feature; MODIFIER silent_mutation Average:65.693; most accessible tissue: Zhenshan97 young leaf, score: 87.443 N N N N
vg0616706040 A -> G LOC_Os06g29260.1 downstream_gene_variant ; 3621.0bp to feature; MODIFIER silent_mutation Average:65.693; most accessible tissue: Zhenshan97 young leaf, score: 87.443 N N N N
vg0616706040 A -> G LOC_Os06g29260.3 intron_variant ; MODIFIER silent_mutation Average:65.693; most accessible tissue: Zhenshan97 young leaf, score: 87.443 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)
vg0616706040 A G 0.0 0.01 0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0616706040 NA 9.64E-16 mr1113 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
vg0616706040 6.38E-06 NA mr1118 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
vg0616706040 NA 5.02E-16 mr1119 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
vg0616706040 NA 1.07E-16 mr1240 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
vg0616706040 1.04E-06 1.80E-18 mr1242 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
vg0616706040 NA 8.98E-14 mr1496 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
vg0616706040 NA 1.26E-06 mr1556 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
vg0616706040 NA 5.94E-21 mr1936 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
vg0616706040 3.22E-07 3.41E-18 mr1113_2 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
vg0616706040 2.18E-07 NA mr1114_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
vg0616706040 6.40E-06 4.24E-18 mr1117_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
vg0616706040 5.79E-09 NA mr1118_2 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
vg0616706040 3.44E-06 7.21E-17 mr1119_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
vg0616706040 5.20E-09 5.57E-24 mr1123_2 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
vg0616706040 3.77E-09 8.18E-22 mr1240_2 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
vg0616706040 5.62E-11 NA mr1242_2 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
vg0616706040 8.56E-06 NA mr1247_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
vg0616706040 8.23E-08 NA mr1495_2 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
vg0616706040 5.08E-09 5.27E-13 mr1496_2 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
vg0616706040 NA 1.19E-06 mr1762_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
vg0616706040 2.04E-08 4.34E-18 mr1936_2 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