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Detailed information for vg0601635891:

Variant ID: vg0601635891 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1635891
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


ATTGCTTTTTTCTGTGTGGATGTGTTGTGTTCTGCTGCTATCTGAATCTTTGTTGCAAGAACACCGTACAAACTGAGTCTGTAACTGATATCCCAAAAAG[T/C]
GTTTGGCTTCACGATTGATGCATCTGCAGACTTGGGTTTTGTGATTGTGTTTTCATGTTTCAACTGGCTGTGTGATCTATGGCTAAGTACATCAATTAAG

Reverse complement sequence

CTTAATTGATGTACTTAGCCATAGATCACACAGCCAGTTGAAACATGAAAACACAATCACAAAACCCAAGTCTGCAGATGCATCAATCGTGAAGCCAAAC[A/G]
CTTTTTGGGATATCAGTTACAGACTCAGTTTGTACGGTGTTCTTGCAACAAAGATTCAGATAGCAGCAGAACACAACACATCCACACAGAAAAAAGCAAT

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 95.00% 5.00% 0.06% 0.00% NA
All Indica  2759 95.70% 4.20% 0.11% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 59.10% 40.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 91.20% 8.20% 0.65% 0.00% NA
Indica III  913 95.80% 4.20% 0.00% 0.00% NA
Indica Intermediate  786 95.00% 5.00% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0601635891 T -> C LOC_Os06g04000.1 3_prime_UTR_variant ; 141.0bp to feature; MODIFIER silent_mutation Average:83.745; most accessible tissue: Minghui63 flag leaf, score: 91.558 N N N N
vg0601635891 T -> C LOC_Os06g03990.1 downstream_gene_variant ; 2262.0bp to feature; MODIFIER silent_mutation Average:83.745; most accessible tissue: Minghui63 flag leaf, score: 91.558 N N N N
vg0601635891 T -> C LOC_Os06g04010.1 downstream_gene_variant ; 633.0bp to feature; MODIFIER silent_mutation Average:83.745; most accessible tissue: Minghui63 flag leaf, score: 91.558 N N N N
vg0601635891 T -> C LOC_Os06g04010.2 downstream_gene_variant ; 637.0bp to feature; MODIFIER silent_mutation Average:83.745; most accessible tissue: Minghui63 flag leaf, score: 91.558 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)
vg0601635891 T C 0.03 0.02 0.03 0.01 0.02 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601635891 NA 2.09E-07 mr1310 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
vg0601635891 NA 2.00E-08 mr1896 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
vg0601635891 4.51E-06 NA mr1256_2 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
vg0601635891 NA 1.31E-06 mr1310_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
vg0601635891 NA 4.05E-06 mr1322_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
vg0601635891 NA 5.28E-06 mr1449_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
vg0601635891 NA 3.92E-06 mr1720_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
vg0601635891 5.40E-06 NA mr1795_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
vg0601635891 NA 5.21E-06 mr1931_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
vg0601635891 NA 2.32E-09 mr1934_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
vg0601635891 NA 1.74E-06 mr1951_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