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Detailed information for vg1102277267:

Variant ID: vg1102277267 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 2277267
Reference Allele: AAlternative Allele: G
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: 259. )

Flanking Sequence (100 bp) in Reference Genome:


ATTCGCGTTCGGCCGGCAGCCGGGCACGGGCCCAACGAATAAGCAGATGGGCCGTGTACAATATTCGGCACGCGAGTAATTGGGCCTTTGAGAAAGTATG[A/G]
TATTGCGGGCTCAATTTTATAACGGACGAGTCCAGAGACGTCTCTTTATCTTATCCTAAACTACAATAGCAGAAATTTTCATCAACTTCCAAAATCAAAT

Reverse complement sequence

ATTTGATTTTGGAAGTTGATGAAAATTTCTGCTATTGTAGTTTAGGATAAGATAAAGAGACGTCTCTGGACTCGTCCGTTATAAAATTGAGCCCGCAATA[T/C]
CATACTTTCTCAAAGGCCCAATTACTCGCGTGCCGAATATTGTACACGGCCCATCTGCTTATTCGTTGGGCCCGTGCCCGGCTGCCGGCCGAACGCGAAT

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 91.00% 7.30% 1.74% 0.00% NA
All Indica  2759 99.50% 0.30% 0.14% 0.00% NA
All Japonica  1512 73.40% 21.70% 4.89% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.50% 0.17% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.30% 0.38% 0.00% NA
Temperate Japonica  767 53.10% 40.80% 6.13% 0.00% NA
Tropical Japonica  504 96.80% 0.80% 2.38% 0.00% NA
Japonica Intermediate  241 89.20% 4.60% 6.22% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 6.70% 4.44% 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
vg1102277267 A -> G LOC_Os11g05180.1 upstream_gene_variant ; 1452.0bp to feature; MODIFIER silent_mutation Average:95.459; most accessible tissue: Minghui63 panicle, score: 99.158 N N N N
vg1102277267 A -> G LOC_Os11g05180.2 upstream_gene_variant ; 1470.0bp to feature; MODIFIER silent_mutation Average:95.459; most accessible tissue: Minghui63 panicle, score: 99.158 N N N N
vg1102277267 A -> G LOC_Os11g05180.3 upstream_gene_variant ; 1481.0bp to feature; MODIFIER silent_mutation Average:95.459; most accessible tissue: Minghui63 panicle, score: 99.158 N N N N
vg1102277267 A -> G LOC_Os11g05160.1 downstream_gene_variant ; 3184.0bp to feature; MODIFIER silent_mutation Average:95.459; most accessible tissue: Minghui63 panicle, score: 99.158 N N N N
vg1102277267 A -> G LOC_Os11g05170.1 downstream_gene_variant ; 135.0bp to feature; MODIFIER silent_mutation Average:95.459; most accessible tissue: Minghui63 panicle, score: 99.158 N N N N
vg1102277267 A -> G LOC_Os11g05170-LOC_Os11g05180 intergenic_region ; MODIFIER silent_mutation Average:95.459; most accessible tissue: Minghui63 panicle, score: 99.158 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)
vg1102277267 A G -0.01 0.01 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1102277267 NA 4.24E-08 mr1002 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
vg1102277267 NA 1.99E-06 mr1002 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
vg1102277267 NA 2.59E-07 mr1163 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
vg1102277267 NA 8.42E-06 mr1555 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
vg1102277267 NA 2.19E-06 mr1627 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
vg1102277267 NA 1.34E-09 mr1002_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
vg1102277267 9.66E-06 1.15E-22 mr1010_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
vg1102277267 NA 8.45E-13 mr1010_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
vg1102277267 NA 7.09E-12 mr1011_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
vg1102277267 NA 9.52E-09 mr1011_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
vg1102277267 NA 5.14E-07 mr1164_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
vg1102277267 NA 3.96E-07 mr1229_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
vg1102277267 NA 1.58E-09 mr1330_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
vg1102277267 NA 5.92E-07 mr1441_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
vg1102277267 NA 3.88E-06 mr1517_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
vg1102277267 NA 2.58E-09 mr1576_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
vg1102277267 NA 1.41E-06 mr1576_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
vg1102277267 NA 1.58E-06 mr1617_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
vg1102277267 NA 1.40E-07 mr1627_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
vg1102277267 NA 7.82E-09 mr1709_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
vg1102277267 NA 9.76E-08 mr1748_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
vg1102277267 NA 7.08E-06 mr1763_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
vg1102277267 NA 3.59E-06 mr1768_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
vg1102277267 NA 3.77E-06 mr1865_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
vg1102277267 NA 1.13E-07 mr1880_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