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Detailed information for vg0605723671:

Variant ID: vg0605723671 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5723671
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.04, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


GCGATTTCCCCCACAACTGTGCAATTAGTTTTTCTTTTTATCTATATTTAATGCTTCATGCATGTGTCCAAAGATTCGATGTGATGTTTTTGGGAAAAAA[T/A]
TTTGGGAACTAAACGGGACCTTATTTGGTTCATGTCGAAGTGCAATGTTCAAAAGGCAACGATGAAACTGTCCAAAAAATGTGATGTCATTGGTTTTAGA

Reverse complement sequence

TCTAAAACCAATGACATCACATTTTTTGGACAGTTTCATCGTTGCCTTTTGAACATTGCACTTCGACATGAACCAAATAAGGTCCCGTTTAGTTCCCAAA[A/T]
TTTTTTCCCAAAAACATCACATCGAATCTTTGGACACATGCATGAAGCATTAAATATAGATAAAAAGAAAAACTAATTGCACAGTTGTGGGGGAAATCGC

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 60.00% 38.10% 1.23% 0.70% NA
All Indica  2759 36.70% 63.00% 0.22% 0.04% NA
All Japonica  1512 97.60% 2.00% 0.40% 0.07% NA
Aus  269 96.30% 3.30% 0.37% 0.00% NA
Indica I  595 11.30% 88.70% 0.00% 0.00% NA
Indica II  465 60.00% 39.60% 0.43% 0.00% NA
Indica III  913 41.00% 58.80% 0.11% 0.11% NA
Indica Intermediate  786 37.30% 62.30% 0.38% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 89.20% 7.90% 2.49% 0.41% NA
VI/Aromatic  96 24.00% 0.00% 44.79% 31.25% NA
Intermediate  90 71.10% 25.60% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0605723671 T -> A LOC_Os06g10950.1 upstream_gene_variant ; 2973.0bp to feature; MODIFIER silent_mutation Average:57.196; most accessible tissue: Zhenshan97 flower, score: 94.089 N N N N
vg0605723671 T -> A LOC_Os06g10960.1 intron_variant ; MODIFIER silent_mutation Average:57.196; most accessible tissue: Zhenshan97 flower, score: 94.089 N N N N
vg0605723671 T -> DEL N N silent_mutation Average:57.196; most accessible tissue: Zhenshan97 flower, score: 94.089 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)
vg0605723671 T A 0.01 -0.01 0.0 -0.01 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605723671 NA 2.01E-06 mr1189 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
vg0605723671 NA 3.25E-06 mr1308 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
vg0605723671 NA 4.39E-06 mr1625 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
vg0605723671 NA 8.18E-09 mr1734 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
vg0605723671 NA 2.15E-06 mr1990 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