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Detailed information for vg1125228571:

Variant ID: vg1125228571 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25228571
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.79, T: 0.21, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGTTCTTCAAATTGATTTGCGCTGGCACGTAAGATGTTTATATTCCCCAGCCCGCTTCCGTCGTTCATTTGACGTATTCCTTGCTCCCGCCTCCGACG[C/T]
CACCGTACATCGCACGGTTGTTGATGTACCGGATGCATGAATGGCTTGGTCGCTCTCCCTCTCTCCATTTCAACCCAACTGCGTGAACTAAACTTAATTT

Reverse complement sequence

AAATTAAGTTTAGTTCACGCAGTTGGGTTGAAATGGAGAGAGGGAGAGCGACCAAGCCATTCATGCATCCGGTACATCAACAACCGTGCGATGTACGGTG[G/A]
CGTCGGAGGCGGGAGCAAGGAATACGTCAAATGAACGACGGAAGCGGGCTGGGGAATATAAACATCTTACGTGCCAGCGCAAATCAATTTGAAGAACTAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.00% 41.70% 0.28% 0.00% NA
All Indica  2759 39.90% 60.00% 0.04% 0.00% NA
All Japonica  1512 84.30% 14.90% 0.79% 0.00% NA
Aus  269 77.00% 23.00% 0.00% 0.00% NA
Indica I  595 37.50% 62.50% 0.00% 0.00% NA
Indica II  465 90.80% 9.20% 0.00% 0.00% NA
Indica III  913 11.70% 88.30% 0.00% 0.00% NA
Indica Intermediate  786 44.50% 55.30% 0.13% 0.00% NA
Temperate Japonica  767 97.30% 2.70% 0.00% 0.00% NA
Tropical Japonica  504 66.30% 32.30% 1.39% 0.00% NA
Japonica Intermediate  241 80.50% 17.40% 2.07% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg1125228571 C -> T LOC_Os11g41960.1 upstream_gene_variant ; 3721.0bp to feature; MODIFIER silent_mutation Average:74.707; most accessible tissue: Zhenshan97 root, score: 90.785 N N N N
vg1125228571 C -> T LOC_Os11g41940.1 downstream_gene_variant ; 1245.0bp to feature; MODIFIER silent_mutation Average:74.707; most accessible tissue: Zhenshan97 root, score: 90.785 N N N N
vg1125228571 C -> T LOC_Os11g41950.1 downstream_gene_variant ; 1798.0bp to feature; MODIFIER silent_mutation Average:74.707; most accessible tissue: Zhenshan97 root, score: 90.785 N N N N
vg1125228571 C -> T LOC_Os11g41940-LOC_Os11g41950 intergenic_region ; MODIFIER silent_mutation Average:74.707; most accessible tissue: Zhenshan97 root, score: 90.785 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)
vg1125228571 C T 0.23 0.15 0.07 -0.02 0.05 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125228571 NA 1.55E-06 mr1094 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
vg1125228571 NA 8.82E-18 mr1133 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
vg1125228571 NA 3.45E-07 mr1133 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
vg1125228571 1.41E-10 NA mr1191 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
vg1125228571 2.66E-11 1.08E-07 mr1191 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
vg1125228571 NA 5.04E-06 mr1598 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
vg1125228571 1.18E-10 NA mr1644 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
vg1125228571 5.31E-12 1.14E-07 mr1644 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
vg1125228571 2.28E-12 NA mr1662 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
vg1125228571 3.78E-08 NA mr1662 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
vg1125228571 NA 7.36E-06 mr1662 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
vg1125228571 NA 6.77E-07 mr1696 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
vg1125228571 NA 8.06E-08 mr1094_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
vg1125228571 NA 5.51E-15 mr1133_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
vg1125228571 NA 3.35E-07 mr1133_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
vg1125228571 NA 6.96E-06 mr1159_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
vg1125228571 2.74E-11 NA mr1191_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
vg1125228571 1.95E-12 7.95E-08 mr1191_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
vg1125228571 3.10E-11 2.21E-06 mr1662_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
vg1125228571 1.34E-06 NA mr1662_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
vg1125228571 1.52E-06 2.95E-06 mr1662_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
vg1125228571 NA 3.80E-06 mr1931_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
vg1125228571 NA 4.14E-07 mr1933_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