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Detailed information for vg0727995401:

Variant ID: vg0727995401 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27995401
Reference Allele: CAlternative Allele: G,T
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGCAACTAGTAACACAGCCACGTCACATGCATGCATGTAGCTAGCAACACAGCCACGAGTAATCAATAGAACGCTCCTGAGAGGAAGCAGGTGGCAGGG[C/G,T]
CCCCTAGCGACGCGGAAGGGTATCTCGTTCCCACGGGATCCCGTGGTCTAGCTATCCTCATTAAGTATTAGCTATTTTTTTTAATTTGATTTGATTAAGC

Reverse complement sequence

GCTTAATCAAATCAAATTAAAAAAAATAGCTAATACTTAATGAGGATAGCTAGACCACGGGATCCCGTGGGAACGAGATACCCTTCCGCGTCGCTAGGGG[G/C,A]
CCCTGCCACCTGCTTCCTCTCAGGAGCGTTCTATTGATTACTCGTGGCTGTGTTGCTAGCTACATGCATGCATGTGACGTGGCTGTGTTACTAGTTGCAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.60% 29.40% 1.90% 4.15% NA
All Indica  2759 43.10% 46.90% 3.19% 6.89% NA
All Japonica  1512 97.20% 2.60% 0.00% 0.20% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 58.70% 27.70% 5.71% 7.90% NA
Indica II  465 30.10% 61.70% 3.01% 5.16% NA
Indica III  913 34.40% 55.10% 2.08% 8.43% NA
Indica Intermediate  786 49.00% 43.00% 2.67% 5.34% NA
Temperate Japonica  767 98.80% 0.80% 0.00% 0.39% NA
Tropical Japonica  504 94.20% 5.80% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 60.40% 39.60% 0.00% 0.00% NA
Intermediate  90 75.60% 18.90% 2.22% 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
vg0727995401 C -> DEL N N silent_mutation Average:84.128; most accessible tissue: Minghui63 flower, score: 96.638 N N N N
vg0727995401 C -> G LOC_Os07g46840.1 upstream_gene_variant ; 446.0bp to feature; MODIFIER silent_mutation Average:84.128; most accessible tissue: Minghui63 flower, score: 96.638 N N N N
vg0727995401 C -> G LOC_Os07g46830.1 downstream_gene_variant ; 2810.0bp to feature; MODIFIER silent_mutation Average:84.128; most accessible tissue: Minghui63 flower, score: 96.638 N N N N
vg0727995401 C -> G LOC_Os07g46830-LOC_Os07g46840 intergenic_region ; MODIFIER silent_mutation Average:84.128; most accessible tissue: Minghui63 flower, score: 96.638 N N N N
vg0727995401 C -> T LOC_Os07g46840.1 upstream_gene_variant ; 446.0bp to feature; MODIFIER N Average:84.128; most accessible tissue: Minghui63 flower, score: 96.638 N N N N
vg0727995401 C -> T LOC_Os07g46830.1 downstream_gene_variant ; 2810.0bp to feature; MODIFIER N Average:84.128; most accessible tissue: Minghui63 flower, score: 96.638 N N N N
vg0727995401 C -> T LOC_Os07g46830-LOC_Os07g46840 intergenic_region ; MODIFIER N Average:84.128; most accessible tissue: Minghui63 flower, score: 96.638 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)
vg0727995401 C G -0.13 -0.07 -0.03 -0.07 -0.09 -0.09
vg0727995401 C T -0.12 -0.09 -0.04 -0.09 -0.17 -0.18

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0727995401 8.54E-06 NA mr1032 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
vg0727995401 NA 2.02E-10 mr1032 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
vg0727995401 2.79E-07 NA mr1165 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
vg0727995401 3.65E-07 3.21E-12 mr1165 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
vg0727995401 NA 4.59E-06 mr1291 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
vg0727995401 NA 6.33E-06 mr1291 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
vg0727995401 NA 6.49E-06 mr1371 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
vg0727995401 1.28E-06 NA mr1478 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
vg0727995401 1.89E-06 2.51E-11 mr1478 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
vg0727995401 NA 7.96E-08 mr1502 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
vg0727995401 NA 1.81E-06 mr1522 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
vg0727995401 NA 5.90E-07 mr1543 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
vg0727995401 NA 3.96E-12 mr1720 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
vg0727995401 NA 1.11E-07 mr1720 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
vg0727995401 NA 1.54E-06 mr1165_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
vg0727995401 4.78E-07 NA mr1457_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
vg0727995401 1.14E-07 7.54E-09 mr1457_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
vg0727995401 NA 1.25E-06 mr1478_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
vg0727995401 NA 4.56E-06 mr1497_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
vg0727995401 NA 8.88E-06 mr1992_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