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Detailed information for vg0221520232:

Variant ID: vg0221520232 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21520232
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.02, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


CGAGGAAAGGAAGGCGCCGTTGCTTCCTACGCCACCAGCTTCGCGCGTGGCTGCGGCGGGGGACAGCGGAGACAAGTGGGCCAGTGGCCGCCAACATCCA[C/A]
ATGAACACCGGGGAAGGGCACCAGGTGTGGTTACCACCGTGGTCCCGACCTCGGTCAAGGGTACGTTCAGTTCACCTGCTCCATCTTTGGGAATTTTGGA

Reverse complement sequence

TCCAAAATTCCCAAAGATGGAGCAGGTGAACTGAACGTACCCTTGACCGAGGTCGGGACCACGGTGGTAACCACACCTGGTGCCCTTCCCCGGTGTTCAT[G/T]
TGGATGTTGGCGGCCACTGGCCCACTTGTCTCCGCTGTCCCCCGCCGCAGCCACGCGCGAAGCTGGTGGCGTAGGAAGCAACGGCGCCTTCCTTTCCTCG

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 69.70% 27.10% 3.15% 0.00% NA
All Indica  2759 51.80% 43.00% 5.22% 0.00% NA
All Japonica  1512 97.00% 3.00% 0.00% 0.00% NA
Aus  269 84.80% 14.50% 0.74% 0.00% NA
Indica I  595 17.10% 71.40% 11.43% 0.00% NA
Indica II  465 65.60% 31.20% 3.23% 0.00% NA
Indica III  913 70.00% 29.00% 0.99% 0.00% NA
Indica Intermediate  786 48.90% 44.50% 6.62% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 93.30% 6.70% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 13.30% 3.33% 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
vg0221520232 C -> A LOC_Os02g35820.1 missense_variant ; p.His146Asn; MODERATE nonsynonymous_codon ; H146N Average:96.647; most accessible tissue: Zhenshan97 young leaf, score: 99.72 unknown unknown TOLERATED 0.84
vg0221520232 C -> A LOC_Os02g35820.2 missense_variant ; p.His146Asn; MODERATE nonsynonymous_codon ; H146N Average:96.647; most accessible tissue: Zhenshan97 young leaf, score: 99.72 unknown unknown TOLERATED 0.32

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)
vg0221520232 C A -0.05 -0.14 -0.12 -0.03 -0.08 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221520232 NA 5.85E-06 mr1461 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
vg0221520232 NA 5.10E-06 mr1734 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
vg0221520232 NA 2.43E-06 mr1911 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
vg0221520232 7.85E-08 7.85E-08 mr1918 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
vg0221520232 NA 6.07E-08 mr1911_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
vg0221520232 NA 2.34E-06 mr1946_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
vg0221520232 NA 2.34E-06 mr1948_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