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Detailed information for vg0700428870:

Variant ID: vg0700428870 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 428870
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.82, C: 0.18, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


GAGATGGTGATGGGTCGTGGCGTGGGTCCATATTGCGCGTTAGATTCTGGCGTGATCTGAGCCATGAGTCCATCCATGGCCCCAACCTAGCTAGTGCGTG[T/C]
TGTGTTCTTTAGTTGGTCGCCACACGGGCAATGCCAAAGTAAAGCCAGGCATGATGCCGGAGGAGGAGGAGGAGAATATGAGATGAGATGAACACTTAAA

Reverse complement sequence

TTTAAGTGTTCATCTCATCTCATATTCTCCTCCTCCTCCTCCGGCATCATGCCTGGCTTTACTTTGGCATTGCCCGTGTGGCGACCAACTAAAGAACACA[A/G]
CACGCACTAGCTAGGTTGGGGCCATGGATGGACTCATGGCTCAGATCACGCCAGAATCTAACGCGCAATATGGACCCACGCCACGACCCATCACCATCTC

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 51.50% 48.30% 0.17% 0.00% NA
All Indica  2759 84.40% 15.40% 0.18% 0.00% NA
All Japonica  1512 0.70% 99.20% 0.07% 0.00% NA
Aus  269 24.90% 74.70% 0.37% 0.00% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 41.90% 57.60% 0.43% 0.00% NA
Indica III  913 98.20% 1.60% 0.11% 0.00% NA
Indica Intermediate  786 83.10% 16.70% 0.25% 0.00% NA
Temperate Japonica  767 0.10% 99.70% 0.13% 0.00% NA
Tropical Japonica  504 1.60% 98.40% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 25.60% 73.30% 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
vg0700428870 T -> C LOC_Os07g01720.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0700428870 T -> C LOC_Os07g01720.1 5_prime_UTR_variant ; 427.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0700428870 T -> C LOC_Os07g01730.1 upstream_gene_variant ; 3214.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0700428870 T -> C LOC_Os07g01710.1 downstream_gene_variant ; 347.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg0700428870 T C -0.06 -0.07 -0.08 0.05 0.0 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0700428870 NA 8.64E-09 mr1110 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
vg0700428870 NA 1.18E-06 mr1216 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
vg0700428870 NA 2.16E-07 mr1216 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
vg0700428870 NA 1.14E-06 mr1110_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
vg0700428870 NA 1.32E-10 mr1158_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
vg0700428870 NA 2.89E-12 mr1383_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
vg0700428870 NA 2.29E-09 mr1478_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
vg0700428870 NA 3.49E-09 mr1889_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