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Detailed information for vg0500580370:

Variant ID: vg0500580370 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 580370
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


CTCGTGCTTGCCTGCCTTAGCTGAGGGACTCAACTCTGTTGACCTTTTGAGCATGAGAGCGACGCACAGCATGCAACCATCAGCTGCTGCCTTTCGATTT[C/A]
TTTCTCCTTCTTCTAGAATTCTACTCGAAAGAAAGAGGAAGGAGGAGAGGAAGATGAAGAGGAGGAGGAAGCCATTAATGGTGGTTGGGGAAGAAGGAAA

Reverse complement sequence

TTTCCTTCTTCCCCAACCACCATTAATGGCTTCCTCCTCCTCTTCATCTTCCTCTCCTCCTTCCTCTTTCTTTCGAGTAGAATTCTAGAAGAAGGAGAAA[G/T]
AAATCGAAAGGCAGCAGCTGATGGTTGCATGCTGTGCGTCGCTCTCATGCTCAAAAGGTCAACAGAGTTGAGTCCCTCAGCTAAGGCAGGCAAGCACGAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.20% 10.80% 0.02% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 68.50% 31.50% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 89.40% 10.60% 0.00% 0.00% NA
Tropical Japonica  504 47.60% 52.20% 0.20% 0.00% NA
Japonica Intermediate  241 45.20% 54.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0500580370 C -> A LOC_Os05g02020.1 5_prime_UTR_variant ; 525.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500580370 C -> A LOC_Os05g02020.2 5_prime_UTR_variant ; 29.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500580370 C -> A LOC_Os05g02010.1 downstream_gene_variant ; 3504.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500580370 C -> A LOC_Os05g02010.2 downstream_gene_variant ; 3504.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500580370 C -> A LOC_Os05g02010.3 downstream_gene_variant ; 3489.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500580370 C -> A LOC_Os05g02010.4 downstream_gene_variant ; 3489.0bp 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)
vg0500580370 C A 0.01 0.02 0.03 -0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500580370 2.35E-06 NA mr1057 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
vg0500580370 NA 1.58E-06 mr1248 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
vg0500580370 NA 2.31E-09 mr1563 Jap_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
vg0500580370 NA 8.80E-08 mr1851 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
vg0500580370 NA 5.58E-12 mr1864 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
vg0500580370 NA 6.27E-10 mr1563_2 Jap_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