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Detailed information for vg1015985151:

Variant ID: vg1015985151 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15985151
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 65. )

Flanking Sequence (100 bp) in Reference Genome:


GGCCCCCAAAATCTAAGGGCCCCCTATGCACATACAGTATATATACTACGTATTGTATAATTCTAGTACACGTGCCATGGATCTATATTAAGTTAGATAG[C/T]
TGAATAGCCTAATATAGAAAATGAATTTTAGTCTATCGTTAGGCCTGTTTTAGTGAAGCTGAAGCAATCTTCATTTGACTCCCGTCGCTTTGCCTTGATC

Reverse complement sequence

GATCAAGGCAAAGCGACGGGAGTCAAATGAAGATTGCTTCAGCTTCACTAAAACAGGCCTAACGATAGACTAAAATTCATTTTCTATATTAGGCTATTCA[G/A]
CTATCTAACTTAATATAGATCCATGGCACGTGTACTAGAATTATACAATACGTAGTATATATACTGTATGTGCATAGGGGGCCCTTAGATTTTGGGGGCC

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 45.70% 40.50% 11.34% 2.45% NA
All Indica  2759 24.90% 58.00% 16.93% 0.18% NA
All Japonica  1512 90.60% 1.00% 1.52% 6.88% NA
Aus  269 7.40% 81.00% 9.67% 1.86% NA
Indica I  595 10.60% 73.90% 15.29% 0.17% NA
Indica II  465 24.10% 56.80% 18.92% 0.22% NA
Indica III  913 28.70% 55.10% 16.21% 0.00% NA
Indica Intermediate  786 31.80% 50.00% 17.81% 0.38% NA
Temperate Japonica  767 96.50% 0.30% 0.26% 3.00% NA
Tropical Japonica  504 89.70% 1.80% 1.79% 6.75% NA
Japonica Intermediate  241 73.90% 1.70% 4.98% 19.50% NA
VI/Aromatic  96 32.30% 55.20% 12.50% 0.00% NA
Intermediate  90 60.00% 28.90% 8.89% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1015985151 C -> T LOC_Os10g30680.1 upstream_gene_variant ; 4626.0bp to feature; MODIFIER silent_mutation Average:67.51; most accessible tissue: Minghui63 root, score: 89.793 N N N N
vg1015985151 C -> T LOC_Os10g30700.1 downstream_gene_variant ; 4629.0bp to feature; MODIFIER silent_mutation Average:67.51; most accessible tissue: Minghui63 root, score: 89.793 N N N N
vg1015985151 C -> T LOC_Os10g30690.1 intron_variant ; MODIFIER silent_mutation Average:67.51; most accessible tissue: Minghui63 root, score: 89.793 N N N N
vg1015985151 C -> DEL N N silent_mutation Average:67.51; most accessible tissue: Minghui63 root, score: 89.793 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)
vg1015985151 C T -0.08 -0.04 -0.03 -0.03 -0.08 -0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015985151 NA 4.15E-09 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
vg1015985151 NA 1.65E-06 mr1667 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
vg1015985151 NA 4.17E-09 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
vg1015985151 2.15E-06 8.41E-10 mr1667_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