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Detailed information for vg0728679648:

Variant ID: vg0728679648 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 28679648
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CTCCTGCACTCCGACCAGGTGCTCTTCAACGGCGGCAGCACGGACAACACGGTCAGGAACTTCTCCTCCAACACGGCGGCGTTCAACAGCGCCTTCACGG[C/T]
GGCCATGGTGAAGATGGGGAACATCTCGCCCTTGACTGGAACCCAGGGGCAGATCAGGCTCAACTGCTCCAAGGTTAACTAGCCGGTGATGACGAGTACG

Reverse complement sequence

CGTACTCGTCATCACCGGCTAGTTAACCTTGGAGCAGTTGAGCCTGATCTGCCCCTGGGTTCCAGTCAAGGGCGAGATGTTCCCCATCTTCACCATGGCC[G/A]
CCGTGAAGGCGCTGTTGAACGCCGCCGTGTTGGAGGAGAAGTTCCTGACCGTGTTGTCCGTGCTGCCGCCGTTGAAGAGCACCTGGTCGGAGTGCAGGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.90% 38.80% 0.02% 0.25% NA
All Indica  2759 94.30% 5.30% 0.04% 0.40% NA
All Japonica  1512 0.90% 99.00% 0.00% 0.07% NA
Aus  269 83.30% 16.70% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.00% 0.17% NA
Indica II  465 95.70% 3.90% 0.00% 0.43% NA
Indica III  913 94.90% 4.90% 0.00% 0.22% NA
Indica Intermediate  786 88.70% 10.40% 0.13% 0.76% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.00% 0.00% 0.20% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 38.90% 61.10% 0.00% 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
vg0728679648 C -> DEL LOC_Os07g48030.1 N frameshift_variant Average:78.533; most accessible tissue: Zhenshan97 young leaf, score: 90.901 N N N N
vg0728679648 C -> T LOC_Os07g48030.1 missense_variant ; p.Ala288Val; MODERATE nonsynonymous_codon ; A288V Average:78.533; most accessible tissue: Zhenshan97 young leaf, score: 90.901 benign 0.433 TOLERATED 0.08

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)
vg0728679648 C T -0.03 -0.02 -0.02 -0.02 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0728679648 NA 6.97E-26 mr1039 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
vg0728679648 NA 3.06E-09 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
vg0728679648 NA 1.74E-06 mr1886 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
vg0728679648 NA 2.29E-27 mr1039_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
vg0728679648 NA 3.87E-18 mr1336_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
vg0728679648 NA 5.96E-32 mr1632_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