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Detailed information for vg0501795080:

Variant ID: vg0501795080 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1795080
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTAACTGGACTACCACGCGTATGTCACGTAGATTAAAATCACCGCGGATTGGGTCGAGGGAGATAATTCGTTCGGTTTGCATAGTTGGGTGTGAAGAAT[G/A]
TCTGGTTTTGCGATTCAGAGGGGTAATTCGTACGTTTTCCTTTTCATAATATTTCAATCCAAATTGTTTTATTATTTCTCCATTATCTAACATATATCTC

Reverse complement sequence

GAGATATATGTTAGATAATGGAGAAATAATAAAACAATTTGGATTGAAATATTATGAAAAGGAAAACGTACGAATTACCCCTCTGAATCGCAAAACCAGA[C/T]
ATTCTTCACACCCAACTATGCAAACCGAACGAATTATCTCCCTCGACCCAATCCGCGGTGATTTTAATCTACGTGACATACGCGTGGTAGTCCAGTTAGC

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 41.10% 32.10% 1.23% 25.52% NA
All Indica  2759 67.70% 12.10% 1.38% 18.81% NA
All Japonica  1512 1.60% 53.60% 1.19% 43.65% NA
Aus  269 8.60% 91.40% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 69.00% 15.10% 1.08% 14.84% NA
Indica III  913 45.50% 17.40% 2.41% 34.72% NA
Indica Intermediate  786 69.50% 12.20% 1.40% 16.92% NA
Temperate Japonica  767 1.20% 75.50% 0.26% 23.08% NA
Tropical Japonica  504 1.60% 31.00% 2.98% 64.48% NA
Japonica Intermediate  241 2.90% 31.10% 0.41% 65.56% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 27.80% 40.00% 2.22% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0501795080 G -> DEL N N silent_mutation Average:61.292; most accessible tissue: Minghui63 young leaf, score: 95.041 N N N N
vg0501795080 G -> A LOC_Os05g03972.1 upstream_gene_variant ; 3798.0bp to feature; MODIFIER silent_mutation Average:61.292; most accessible tissue: Minghui63 young leaf, score: 95.041 N N N N
vg0501795080 G -> A LOC_Os05g04000.1 upstream_gene_variant ; 909.0bp to feature; MODIFIER silent_mutation Average:61.292; most accessible tissue: Minghui63 young leaf, score: 95.041 N N N N
vg0501795080 G -> A LOC_Os05g04010.1 downstream_gene_variant ; 4601.0bp to feature; MODIFIER silent_mutation Average:61.292; most accessible tissue: Minghui63 young leaf, score: 95.041 N N N N
vg0501795080 G -> A LOC_Os05g03972-LOC_Os05g04000 intergenic_region ; MODIFIER silent_mutation Average:61.292; most accessible tissue: Minghui63 young leaf, score: 95.041 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)
vg0501795080 G A 0.01 0.02 0.02 0.01 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501795080 NA 9.61E-06 mr1189 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
vg0501795080 NA 1.84E-13 mr1531 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
vg0501795080 NA 7.62E-17 mr1807 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
vg0501795080 3.41E-06 3.47E-07 mr1030_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
vg0501795080 1.17E-06 1.01E-06 mr1030_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
vg0501795080 NA 1.60E-06 mr1322_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
vg0501795080 NA 5.10E-07 mr1358_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
vg0501795080 NA 1.03E-07 mr1446_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
vg0501795080 NA 6.63E-06 mr1524_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
vg0501795080 NA 3.12E-07 mr1527_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
vg0501795080 9.41E-06 6.09E-17 mr1578_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
vg0501795080 6.76E-06 9.63E-06 mr1578_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
vg0501795080 NA 1.42E-06 mr1623_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
vg0501795080 NA 5.80E-13 mr1717_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
vg0501795080 NA 2.74E-09 mr1754_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
vg0501795080 NA 1.39E-06 mr1754_2 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
vg0501795080 NA 3.94E-07 mr1819_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
vg0501795080 NA 4.11E-07 mr1910_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
vg0501795080 NA 6.12E-11 mr1946_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
vg0501795080 NA 6.12E-11 mr1948_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
vg0501795080 9.84E-06 NA mr1952_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
vg0501795080 1.72E-06 1.19E-08 mr1952_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
vg0501795080 5.70E-06 NA mr1965_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
vg0501795080 4.70E-06 4.70E-06 mr1965_2 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