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Detailed information for vg0628487999:

Variant ID: vg0628487999 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 28487999
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGGAAGGCGGATATTCGCCGGCGCCGGTGGGTCTAGCCATTTCCCAACCTTGCCCTATTGGTGGGTCCGCTTGGGGCTAAATACACGAACAGATTGCGA[T/A]
TTTTTCTGCGAGGGGATCGGTGATGCTGCGCGTGCACCGCGCTGATCTGGGTGTGCTGCGGCGGCGCAACCCCGTTCTGGGTTGCATCCTCGTCGGCGGC

Reverse complement sequence

GCCGCCGACGAGGATGCAACCCAGAACGGGGTTGCGCCGCCGCAGCACACCCAGATCAGCGCGGTGCACGCGCAGCATCACCGATCCCCTCGCAGAAAAA[A/T]
TCGCAATCTGTTCGTGTATTTAGCCCCAAGCGGACCCACCAATAGGGCAAGGTTGGGAAATGGCTAGACCCACCGGCGCCGGCGAATATCCGCCTTCCCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.80% 8.20% 0.00% 0.00% NA
All Indica  2759 97.40% 2.60% 0.00% 0.00% NA
All Japonica  1512 97.50% 2.50% 0.00% 0.00% NA
Aus  269 24.50% 75.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 95.00% 5.00% 0.00% 0.00% NA
Indica Intermediate  786 97.50% 2.50% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 94.00% 6.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 33.30% 66.70% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0628487999 T -> A LOC_Os06g46950.1 downstream_gene_variant ; 3375.0bp to feature; MODIFIER silent_mutation Average:97.26; most accessible tissue: Minghui63 flower, score: 98.714 N N N N
vg0628487999 T -> A LOC_Os06g46970.1 downstream_gene_variant ; 1961.0bp to feature; MODIFIER silent_mutation Average:97.26; most accessible tissue: Minghui63 flower, score: 98.714 N N N N
vg0628487999 T -> A LOC_Os06g46960.1 intron_variant ; MODIFIER silent_mutation Average:97.26; most accessible tissue: Minghui63 flower, score: 98.714 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)
vg0628487999 T A -0.02 -0.02 -0.03 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0628487999 NA 4.06E-06 mr1262 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
vg0628487999 NA 5.67E-06 mr1633 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
vg0628487999 NA 8.12E-06 mr1158_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