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Detailed information for vg1004252046:

Variant ID: vg1004252046 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4252046
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, A: 0.10, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


ATGATGGAAGGGAAGGGCGTGCTGGTGAACAGCTTCGACTGGCTGGAGCCCAAGGCCCTGAAAGCGCTCGCCGCCGGTGTCTGCGTGCCCGACAAGCCCA[C/A]
GCCGAGCGTCTACTGCGTCGGGCCACTGGTCGACACCGGCAACAAGGTAGGGAGCGGCGCCGAGAGGCGCCATGCGTGCCTCGTGTGGCTTGACGCCCAG

Reverse complement sequence

CTGGGCGTCAAGCCACACGAGGCACGCATGGCGCCTCTCGGCGCCGCTCCCTACCTTGTTGCCGGTGTCGACCAGTGGCCCGACGCAGTAGACGCTCGGC[G/T]
TGGGCTTGTCGGGCACGCAGACACCGGCGGCGAGCGCTTTCAGGGCCTTGGGCTCCAGCCAGTCGAAGCTGTTCACCAGCACGCCCTTCCCTTCCATCAT

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 64.60% 35.20% 0.11% 0.11% NA
All Indica  2759 69.80% 29.90% 0.11% 0.18% NA
All Japonica  1512 69.20% 30.70% 0.07% 0.00% NA
Aus  269 4.10% 95.50% 0.37% 0.00% NA
Indica I  595 58.50% 41.20% 0.17% 0.17% NA
Indica II  465 71.60% 28.00% 0.00% 0.43% NA
Indica III  913 72.90% 27.10% 0.00% 0.00% NA
Indica Intermediate  786 73.50% 26.00% 0.25% 0.25% NA
Temperate Japonica  767 84.40% 15.50% 0.13% 0.00% NA
Tropical Japonica  504 53.40% 46.60% 0.00% 0.00% NA
Japonica Intermediate  241 54.40% 45.60% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg1004252046 C -> A LOC_Os10g07970.1 missense_variant ; p.Thr167Lys; MODERATE nonsynonymous_codon ; T167N Average:82.53; most accessible tissue: Zhenshan97 flag leaf, score: 88.022 benign 0.332 DELETERIOUS 0.01
vg1004252046 C -> A LOC_Os10g07970.1 missense_variant ; p.Thr167Lys; MODERATE nonsynonymous_codon ; T167K Average:82.53; most accessible tissue: Zhenshan97 flag leaf, score: 88.022 benign 0.32 DELETERIOUS 0.02
vg1004252046 C -> DEL LOC_Os10g07970.1 N frameshift_variant Average:82.53; most accessible tissue: Zhenshan97 flag leaf, score: 88.022 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)
vg1004252046 C A 0.01 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004252046 NA 1.34E-06 mr1471 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
vg1004252046 NA 2.03E-07 mr1047_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
vg1004252046 2.24E-07 8.60E-10 mr1188_2 Jap_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