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Detailed information for vg0722039270:

Variant ID: vg0722039270 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22039270
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTGTCGGATGATCTATGCTCCTCCAGTAGACTATGGATGAATTGGTGGCATCCATGAGGTCGAGGCTACCGCCGTCCTGGATGACGGCAACGGTGGAG[T/C]
TGGAGGCCACACTTACGTTGGTCGACCACAGCTGCCTGTTCTTGGATTGATCAAGGAGGACAAGATTGCCATCGCTGCCGATGGACAAGGATGCGGTGGT

Reverse complement sequence

ACCACCGCATCCTTGTCCATCGGCAGCGATGGCAATCTTGTCCTCCTTGATCAATCCAAGAACAGGCAGCTGTGGTCGACCAACGTAAGTGTGGCCTCCA[A/G]
CTCCACCGTTGCCGTCATCCAGGACGGCGGTAGCCTCGACCTCATGGATGCCACCAATTCATCCATAGTCTACTGGAGGAGCATAGATCATCCGACAAAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.10% 10.90% 0.02% 0.00% NA
All Indica  2759 87.40% 12.60% 0.00% 0.00% NA
All Japonica  1512 94.30% 5.70% 0.00% 0.00% NA
Aus  269 74.00% 25.70% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 80.60% 19.40% 0.00% 0.00% NA
Indica III  913 80.90% 19.10% 0.00% 0.00% NA
Indica Intermediate  786 89.60% 10.40% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 86.30% 13.70% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0722039270 T -> C LOC_Os07g36780.1 missense_variant ; p.Asn122Ser; MODERATE nonsynonymous_codon Average:89.652; most accessible tissue: Minghui63 flag leaf, score: 94.11 benign 0.288 TOLERATED 0.56

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)
vg0722039270 T C -0.04 0.0 0.02 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722039270 NA 7.21E-08 mr1188 Ind_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
vg0722039270 NA 5.59E-08 mr1188_2 Ind_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