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Detailed information for vg1105998802:

Variant ID: vg1105998802 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5998802
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


TCGTCGGCACCACCACGGCGGCGCCGTGCGATCCCCTCTGCATATGTACTACGTCACACTAATACACACTATCACTAGTTCACTGCTACTGATCTAACTA[A/G]
CTCGACCATCACCAAAATGAGGATCGAAATTAATCAAATGCATGTCCCTTACTACGACATTTGCATGGTATATATATGTGTCCAGCTGGAGCGGCGGCCG

Reverse complement sequence

CGGCCGCCGCTCCAGCTGGACACATATATATACCATGCAAATGTCGTAGTAAGGGACATGCATTTGATTAATTTCGATCCTCATTTTGGTGATGGTCGAG[T/C]
TAGTTAGATCAGTAGCAGTGAACTAGTGATAGTGTGTATTAGTGTGACGTAGTACATATGCAGAGGGGATCGCACGGCGCCGCCGTGGTGGTGCCGACGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 46.30% 38.60% 8.06% 7.00% NA
All Indica  2759 28.10% 50.40% 11.05% 10.47% NA
All Japonica  1512 82.10% 15.70% 2.05% 0.13% NA
Aus  269 12.60% 59.50% 14.13% 13.75% NA
Indica I  595 29.10% 40.70% 20.84% 9.41% NA
Indica II  465 18.70% 58.30% 12.90% 10.11% NA
Indica III  913 29.60% 54.40% 2.85% 13.14% NA
Indica Intermediate  786 31.20% 48.30% 12.09% 8.40% NA
Temperate Japonica  767 71.10% 25.00% 3.78% 0.13% NA
Tropical Japonica  504 96.20% 3.20% 0.40% 0.20% NA
Japonica Intermediate  241 88.00% 12.00% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 9.40% 1.04% 1.04% NA
Intermediate  90 58.90% 32.20% 6.67% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105998802 A -> DEL N N silent_mutation Average:72.474; most accessible tissue: Zhenshan97 flag leaf, score: 85.761 N N N N
vg1105998802 A -> G LOC_Os11g10870.1 downstream_gene_variant ; 1261.0bp to feature; MODIFIER silent_mutation Average:72.474; most accessible tissue: Zhenshan97 flag leaf, score: 85.761 N N N N
vg1105998802 A -> G LOC_Os11g10890.1 downstream_gene_variant ; 3105.0bp to feature; MODIFIER silent_mutation Average:72.474; most accessible tissue: Zhenshan97 flag leaf, score: 85.761 N N N N
vg1105998802 A -> G LOC_Os11g10880.1 intron_variant ; MODIFIER silent_mutation Average:72.474; most accessible tissue: Zhenshan97 flag leaf, score: 85.761 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)
vg1105998802 A G 0.0 0.0 -0.01 0.0 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105998802 4.83E-06 6.48E-06 mr1295 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