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Detailed information for vg1207220741:

Variant ID: vg1207220741 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7220741
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


AATAGTTAATTTCCTTAATTCTGTCATGATCTGATGCAGCTTCCAAAATTCCCCAAGTCTGAAAGAGAGCTCAATGATACATCCATTCAGAACATTCAGG[C/T]
GGACATGTGCTACTTCATCCACCGTGAGTGCGCACATCAGCCTGGGCGGTTTTTCGACAACGAAGGAGTCTTAGCCCTGCCGGAGAACGAATCCCTGTCT

Reverse complement sequence

AGACAGGGATTCGTTCTCCGGCAGGGCTAAGACTCCTTCGTTGTCGAAAAACCGCCCAGGCTGATGTGCGCACTCACGGTGGATGAAGTAGCACATGTCC[G/A]
CCTGAATGTTCTGAATGGATGTATCATTGAGCTCTCTTTCAGACTTGGGGAATTTTGGAAGCTGCATCAGATCATGACAGAATTAAGGAAATTAACTATT

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 88.30% 11.70% 0.04% 0.00% NA
All Indica  2759 87.00% 12.90% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 46.80% 53.20% 0.00% 0.00% NA
Indica I  595 89.20% 10.80% 0.00% 0.00% NA
Indica II  465 90.50% 9.50% 0.00% 0.00% NA
Indica III  913 88.20% 11.60% 0.22% 0.00% NA
Indica Intermediate  786 81.80% 18.20% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 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 50.00% 50.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1207220741 C -> T LOC_Os12g13020.1 missense_variant ; p.Ala852Val; MODERATE nonsynonymous_codon ; A852V Average:17.82; most accessible tissue: Minghui63 young leaf, score: 23.613 benign 0.181 TOLERATED 0.48

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207220741 3.20E-06 7.95E-06 mr1324 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
vg1207220741 6.53E-06 NA mr1335 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
vg1207220741 2.10E-06 4.55E-06 mr1335 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
vg1207220741 NA 2.95E-07 mr1347 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
vg1207220741 9.83E-06 8.89E-06 mr1482 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
vg1207220741 2.70E-06 2.53E-06 mr1590 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
vg1207220741 6.01E-06 NA mr1660 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
vg1207220741 5.03E-06 NA mr1660 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
vg1207220741 NA 6.79E-07 mr1705 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
vg1207220741 4.57E-07 4.40E-09 mr1815 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
vg1207220741 4.94E-06 NA mr1815 Ind_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
vg1207220741 8.74E-07 9.95E-06 mr1964 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