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Detailed information for vg1125185237:

Variant ID: vg1125185237 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25185237
Reference Allele: CAlternative Allele: T,A
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.02, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GGGAGGACGGGTTCACACTACACACGTGCACGTTTCGGGGAAACGAATGAGTCGGCTGGGCCCACCCGTCAGTCTAAATAGCCGCGATGCTGCCTACTCC[C/T,A]
TCCGTTAAAAAAAACTCAATTCCTATATTTCTGTGTTTAACGTTTGACCATCCGTCTTATTTTAAAAAATATATAAAAAAAATAAACAGATAAATCATGC

Reverse complement sequence

GCATGATTTATCTGTTTATTTTTTTTATATATTTTTTAAAATAAGACGGATGGTCAAACGTTAAACACAGAAATATAGGAATTGAGTTTTTTTTAACGGA[G/A,T]
GGAGTAGGCAGCATCGCGGCTATTTAGACTGACGGGTGGGCCCAGCCGACTCATTCGTTTCCCCGAAACGTGCACGTGTGTAGTGTGAACCCGTCCTCCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.60% 49.10% 0.28% 0.00% A: 0.04%
All Indica  2759 76.90% 22.60% 0.40% 0.00% A: 0.07%
All Japonica  1512 14.10% 85.80% 0.07% 0.00% NA
Aus  269 5.60% 94.40% 0.00% 0.00% NA
Indica I  595 62.90% 37.00% 0.17% 0.00% NA
Indica II  465 61.30% 38.50% 0.22% 0.00% NA
Indica III  913 92.70% 7.00% 0.22% 0.00% A: 0.11%
Indica Intermediate  786 78.50% 20.50% 0.89% 0.00% A: 0.13%
Temperate Japonica  767 2.70% 97.30% 0.00% 0.00% NA
Tropical Japonica  504 31.20% 68.70% 0.20% 0.00% NA
Japonica Intermediate  241 14.50% 85.50% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 41.10% 57.80% 1.11% 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
vg1125185237 C -> T LOC_Os11g41880.1 upstream_gene_variant ; 1761.0bp to feature; MODIFIER silent_mutation Average:94.764; most accessible tissue: Callus, score: 99.39 N N N N
vg1125185237 C -> T LOC_Os11g41875.2 upstream_gene_variant ; 4965.0bp to feature; MODIFIER silent_mutation Average:94.764; most accessible tissue: Callus, score: 99.39 N N N N
vg1125185237 C -> T LOC_Os11g41880-LOC_Os11g41890 intergenic_region ; MODIFIER silent_mutation Average:94.764; most accessible tissue: Callus, score: 99.39 N N N N
vg1125185237 C -> A LOC_Os11g41880.1 upstream_gene_variant ; 1761.0bp to feature; MODIFIER silent_mutation Average:94.764; most accessible tissue: Callus, score: 99.39 N N N N
vg1125185237 C -> A LOC_Os11g41875.2 upstream_gene_variant ; 4965.0bp to feature; MODIFIER silent_mutation Average:94.764; most accessible tissue: Callus, score: 99.39 N N N N
vg1125185237 C -> A LOC_Os11g41880-LOC_Os11g41890 intergenic_region ; MODIFIER silent_mutation Average:94.764; most accessible tissue: Callus, score: 99.39 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)
vg1125185237 C A 0.03 0.06 0.08 0.0 0.04 0.05
vg1125185237 C T 0.0 0.01 0.03 0.0 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125185237 NA 2.66E-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
vg1125185237 1.26E-08 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
vg1125185237 9.56E-09 1.47E-10 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
vg1125185237 2.50E-06 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
vg1125185237 2.80E-07 3.01E-09 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
vg1125185237 3.33E-19 2.26E-12 mr1662 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
vg1125185237 5.86E-13 6.42E-14 mr1662 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
vg1125185237 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
vg1125185237 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
vg1125185237 NA 2.32E-06 mr1745 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
vg1125185237 NA 5.33E-08 mr1925 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
vg1125185237 8.00E-06 3.00E-20 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
vg1125185237 NA 1.42E-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
vg1125185237 4.57E-10 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
vg1125185237 6.72E-11 2.34E-16 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
vg1125185237 2.52E-16 1.61E-09 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
vg1125185237 7.53E-11 1.51E-14 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
vg1125185237 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
vg1125185237 NA 1.29E-12 mr1667_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
vg1125185237 NA 2.10E-06 mr1745_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