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Detailed information for vg1017311370:

Variant ID: vg1017311370 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 17311370
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, T: 0.09, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:


TTAATGTGGATACCTCTATATTAATGATTGACGTAATATGTTTCTGATAGTGGAAATGGGGCTGTAGGATCAGAGACAATGGCTGTGTTTAGTTGAGGGA[A/T]
AGTTTGGATTTTGGTTGAAATTGAAGATAATGTGACTGAAAAGTTGTGTGTGTATGACAGGTTGATGTGATGAAAAAGGACTGAAGTTTGGATCCAAATT

Reverse complement sequence

AATTTGGATCCAAACTTCAGTCCTTTTTCATCACATCAACCTGTCATACACACACAACTTTTCAGTCACATTATCTTCAATTTCAACCAAAATCCAAACT[T/A]
TCCCTCAACTAAACACAGCCATTGTCTCTGATCCTACAGCCCCATTTCCACTATCAGAAACATATTACGTCAATCATTAATATAGAGGTATCCACATTAA

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 50.40% 28.00% 1.84% 19.76% NA
All Indica  2759 68.00% 3.20% 1.01% 27.80% NA
All Japonica  1512 8.90% 77.40% 3.70% 9.92% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 80.50% 1.70% 0.67% 17.14% NA
Indica II  465 73.30% 5.20% 1.08% 20.43% NA
Indica III  913 57.90% 2.00% 1.64% 38.44% NA
Indica Intermediate  786 66.90% 4.70% 0.51% 27.86% NA
Temperate Japonica  767 2.00% 97.30% 0.13% 0.65% NA
Tropical Japonica  504 7.30% 56.20% 10.32% 26.19% NA
Japonica Intermediate  241 34.40% 58.90% 1.24% 5.39% NA
VI/Aromatic  96 69.80% 30.20% 0.00% 0.00% NA
Intermediate  90 42.20% 35.60% 3.33% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1017311370 A -> T LOC_Os10g33040.1 upstream_gene_variant ; 891.0bp to feature; MODIFIER silent_mutation Average:83.371; most accessible tissue: Zhenshan97 flag leaf, score: 96.532 N N N N
vg1017311370 A -> T LOC_Os10g33050.1 downstream_gene_variant ; 4818.0bp to feature; MODIFIER silent_mutation Average:83.371; most accessible tissue: Zhenshan97 flag leaf, score: 96.532 N N N N
vg1017311370 A -> T LOC_Os10g33030-LOC_Os10g33040 intergenic_region ; MODIFIER silent_mutation Average:83.371; most accessible tissue: Zhenshan97 flag leaf, score: 96.532 N N N N
vg1017311370 A -> DEL N N silent_mutation Average:83.371; most accessible tissue: Zhenshan97 flag leaf, score: 96.532 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)
vg1017311370 A T 0.0 0.01 -0.01 -0.01 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1017311370 2.03E-06 NA mr1218 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
vg1017311370 NA 4.75E-22 mr1548 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
vg1017311370 NA 2.74E-26 mr1617 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
vg1017311370 NA 1.38E-06 mr1815 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