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Detailed information for vg0507129275:

Variant ID: vg0507129275 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7129275
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


AAAAGCTGGATGACGGCATCACCGAGCTCGCCAGTTCCGCCGAGAGCACCGACTTCATTTCCCGCCACCATCTTCCCTTCTCCTCACATGTGTCTCTCCC[C/T]
AGGTTGCCACCAACGCCCCGTCGAGCTCGTGGTGGTGACCTTGCTTACAACGGCCACTCGTTGGATGCCTGTCACCGCCTACATGTGTTGTGGAGGCGTC

Reverse complement sequence

GACGCCTCCACAACACATGTAGGCGGTGACAGGCATCCAACGAGTGGCCGTTGTAAGCAAGGTCACCACCACGAGCTCGACGGGGCGTTGGTGGCAACCT[G/A]
GGGAGAGACACATGTGAGGAGAAGGGAAGATGGTGGCGGGAAATGAAGTCGGTGCTCTCGGCGGAACTGGCGAGCTCGGTGATGCCGTCATCCAGCTTTT

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 60.40% 38.70% 0.08% 0.87% NA
All Indica  2759 60.90% 37.90% 0.11% 1.12% NA
All Japonica  1512 60.30% 39.40% 0.00% 0.40% NA
Aus  269 79.90% 20.10% 0.00% 0.00% NA
Indica I  595 83.50% 16.50% 0.00% 0.00% NA
Indica II  465 26.90% 71.40% 0.00% 1.72% NA
Indica III  913 58.70% 40.00% 0.11% 1.20% NA
Indica Intermediate  786 66.30% 31.90% 0.25% 1.53% NA
Temperate Japonica  767 91.40% 8.50% 0.00% 0.13% NA
Tropical Japonica  504 13.50% 85.70% 0.00% 0.79% NA
Japonica Intermediate  241 58.90% 40.70% 0.00% 0.41% NA
VI/Aromatic  96 2.10% 95.80% 1.04% 1.04% NA
Intermediate  90 51.10% 45.60% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0507129275 C -> T LOC_Os05g12380.1 downstream_gene_variant ; 2123.0bp to feature; MODIFIER silent_mutation Average:85.767; most accessible tissue: Zhenshan97 panicle, score: 96.13 N N N N
vg0507129275 C -> T LOC_Os05g12390.1 downstream_gene_variant ; 1750.0bp to feature; MODIFIER silent_mutation Average:85.767; most accessible tissue: Zhenshan97 panicle, score: 96.13 N N N N
vg0507129275 C -> T LOC_Os05g12400.1 downstream_gene_variant ; 4752.0bp to feature; MODIFIER silent_mutation Average:85.767; most accessible tissue: Zhenshan97 panicle, score: 96.13 N N N N
vg0507129275 C -> T LOC_Os05g12380-LOC_Os05g12390 intergenic_region ; MODIFIER silent_mutation Average:85.767; most accessible tissue: Zhenshan97 panicle, score: 96.13 N N N N
vg0507129275 C -> DEL N N silent_mutation Average:85.767; most accessible tissue: Zhenshan97 panicle, score: 96.13 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)
vg0507129275 C T -0.06 -0.05 -0.06 -0.04 -0.06 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507129275 NA 7.86E-17 Grain_thickness Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0507129275 NA 5.34E-13 Grain_width Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0507129275 3.56E-06 NA mr1195 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
vg0507129275 6.38E-06 6.72E-09 mr1195 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
vg0507129275 NA 2.14E-06 mr1401 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
vg0507129275 3.96E-07 NA mr1531 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
vg0507129275 1.83E-06 6.20E-10 mr1531 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
vg0507129275 NA 4.14E-07 mr1551 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
vg0507129275 5.25E-44 1.99E-79 mr1593 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
vg0507129275 1.26E-32 6.06E-62 mr1593 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
vg0507129275 1.49E-16 4.67E-39 mr1593 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
vg0507129275 NA 4.92E-07 mr1723 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
vg0507129275 NA 8.39E-06 mr1887 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
vg0507129275 8.99E-10 NA mr1195_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
vg0507129275 5.46E-10 3.06E-22 mr1195_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
vg0507129275 NA 1.86E-06 mr1268_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
vg0507129275 NA 9.58E-09 mr1327_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
vg0507129275 NA 3.93E-07 mr1378_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
vg0507129275 NA 9.91E-08 mr1482_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
vg0507129275 5.32E-06 NA mr1531_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
vg0507129275 4.39E-06 3.64E-10 mr1531_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
vg0507129275 8.09E-51 2.81E-104 mr1593_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
vg0507129275 2.86E-34 2.20E-74 mr1593_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
vg0507129275 4.21E-24 9.08E-61 mr1593_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
vg0507129275 NA 1.80E-08 mr1627_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
vg0507129275 3.78E-09 1.98E-23 mr1807_2 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
vg0507129275 4.07E-09 7.79E-14 mr1807_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