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Detailed information for vg0721912854:

Variant ID: vg0721912854 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21912854
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TGATCGGTTTCAGCTTTGCCACTTGGTTTAGCAGCCAACTAACACCAAACCAAAAATCTCCAATCACAGATATCCACCAGAAAAACATGCCATCGGCGTA[C/T]
GGGTGCCTGATACGCCATATGAAAAATAGGACGATAGCAACCAATCTGACCAATGTCAATAACCTGTTGCAAAGAAATGGAAAAAAAATGGTTAGAATAC

Reverse complement sequence

GTATTCTAACCATTTTTTTTCCATTTCTTTGCAACAGGTTATTGACATTGGTCAGATTGGTTGCTATCGTCCTATTTTTCATATGGCGTATCAGGCACCC[G/A]
TACGCCGATGGCATGTTTTTCTGGTGGATATCTGTGATTGGAGATTTTTGGTTTGGTGTTAGTTGGCTGCTAAACCAAGTGGCAAAGCTGAAACCGATCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.70% 23.20% 0.15% 0.00% NA
All Indica  2759 68.50% 31.20% 0.22% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 19.00% 80.70% 0.37% 0.00% NA
Indica I  595 12.80% 86.90% 0.34% 0.00% NA
Indica II  465 88.00% 11.60% 0.43% 0.00% NA
Indica III  913 93.80% 6.20% 0.00% 0.00% NA
Indica Intermediate  786 70.00% 29.80% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0721912854 C -> T LOC_Os07g36630.1 synonymous_variant ; p.Pro114Pro; LOW synonymous_codon Average:63.226; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721912854 NA 8.57E-11 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0721912854 NA 2.99E-08 mr1222 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
vg0721912854 NA 3.41E-09 mr1565 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
vg0721912854 NA 9.43E-08 mr1857 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
vg0721912854 NA 1.17E-08 mr1222_2 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
vg0721912854 NA 9.18E-09 mr1962_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