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Detailed information for vg1226947846:

Variant ID: vg1226947846 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 26947846
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGCACATGCCATGCTGCTGAAAAAGTCTAGATTATTTCTTAATAACTGTTGAGAAATCTAGATGAAGAGAGAATATACTGGAACTTCATACATGAATA[G/C]
CATTGCAGCAGTAACTAATATTATTTTTACATTTGAAAGAGTTGCTATACGGATTCAGTAAGCTAGATGCACACAACTAAATTGAATAATGTACTATTAT

Reverse complement sequence

ATAATAGTACATTATTCAATTTAGTTGTGTGCATCTAGCTTACTGAATCCGTATAGCAACTCTTTCAAATGTAAAAATAATATTAGTTACTGCTGCAATG[C/G]
TATTCATGTATGAAGTTCCAGTATATTCTCTCTTCATCTAGATTTCTCAACAGTTATTAAGAAATAATCTAGACTTTTTCAGCAGCATGGCATGTGCCAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.20% 40.10% 0.61% 0.04% NA
All Indica  2759 80.80% 18.70% 0.43% 0.04% NA
All Japonica  1512 15.20% 83.70% 0.99% 0.07% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 43.20% 55.50% 1.34% 0.00% NA
Indica II  465 94.60% 5.20% 0.22% 0.00% NA
Indica III  913 92.90% 6.90% 0.11% 0.11% NA
Indica Intermediate  786 87.00% 12.70% 0.25% 0.00% NA
Temperate Japonica  767 25.90% 72.40% 1.69% 0.00% NA
Tropical Japonica  504 3.00% 96.80% 0.00% 0.20% NA
Japonica Intermediate  241 6.60% 92.50% 0.83% 0.00% NA
VI/Aromatic  96 22.90% 77.10% 0.00% 0.00% NA
Intermediate  90 60.00% 37.80% 2.22% 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
vg1226947846 G -> C LOC_Os12g43410-LOC_Os12g43440 intergenic_region ; MODIFIER silent_mutation Average:54.092; most accessible tissue: Zhenshan97 root, score: 92.529 N N N N
vg1226947846 G -> DEL N N silent_mutation Average:54.092; most accessible tissue: Zhenshan97 root, score: 92.529 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)
vg1226947846 G C 0.0 0.0 0.0 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1226947846 NA 1.72E-14 mr1062 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
vg1226947846 NA 9.37E-08 mr1201 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
vg1226947846 NA 1.45E-06 mr1219 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
vg1226947846 NA 1.10E-08 mr1274 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
vg1226947846 NA 3.51E-10 mr1332 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
vg1226947846 NA 6.39E-10 mr1336 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
vg1226947846 NA 5.41E-08 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
vg1226947846 NA 4.53E-06 mr1128_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
vg1226947846 NA 3.49E-06 mr1152_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
vg1226947846 3.31E-06 8.63E-07 mr1154_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
vg1226947846 NA 4.73E-08 mr1170_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
vg1226947846 NA 2.88E-06 mr1201_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
vg1226947846 NA 5.75E-06 mr1204_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
vg1226947846 NA 6.58E-06 mr1219_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
vg1226947846 NA 3.20E-08 mr1600_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
vg1226947846 NA 3.11E-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