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Detailed information for vg1205810555:

Variant ID: vg1205810555 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 5810555
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GTCACCACAACGACACTCTGGATGTTCCCGCCATGTGGGGAGTCCTAGGGGGTTTACCTGCCATTCTAAAGCTTCTGCAGCAATCCGACGTTCATGCTCA[T/C]
CCTTCCGCCTGAGGTAGTCCGATCTTGATTCACTACGTGCATATGGACGTGTTCCGTCGTTTTGTGGGTTCTCTGTATCTACCCACTCAATGTAGTTGCA

Reverse complement sequence

TGCAACTACATTGAGTGGGTAGATACAGAGAACCCACAAAACGACGGAACACGTCCATATGCACGTAGTGAATCAAGATCGGACTACCTCAGGCGGAAGG[A/G]
TGAGCATGAACGTCGGATTGCTGCAGAAGCTTTAGAATGGCAGGTAAACCCCCTAGGACTCCCCACATGGCGGGAACATCCAGAGTGTCGTTGTGGTGAC

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 93.70% 0.90% 1.29% 4.08% NA
All Indica  2759 94.20% 1.50% 1.16% 3.15% NA
All Japonica  1512 95.20% 0.00% 1.79% 2.98% NA
Aus  269 98.50% 0.00% 0.37% 1.12% NA
Indica I  595 86.20% 2.40% 2.18% 9.24% NA
Indica II  465 97.60% 0.00% 1.08% 1.29% NA
Indica III  913 97.50% 2.00% 0.55% 0.00% NA
Indica Intermediate  786 94.30% 1.30% 1.15% 3.31% NA
Temperate Japonica  767 91.90% 0.00% 2.74% 5.35% NA
Tropical Japonica  504 98.40% 0.00% 1.19% 0.40% NA
Japonica Intermediate  241 99.20% 0.00% 0.00% 0.83% NA
VI/Aromatic  96 45.80% 1.00% 0.00% 53.12% NA
Intermediate  90 91.10% 0.00% 1.11% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1205810555 T -> C LOC_Os12g10800.1 missense_variant ; p.Asp1388Gly; MODERATE nonsynonymous_codon ; D1388G Average:21.674; most accessible tissue: Callus, score: 29.978 unknown unknown DELETERIOUS 0.02
vg1205810555 T -> DEL LOC_Os12g10800.1 N frameshift_variant Average:21.674; most accessible tissue: Callus, score: 29.978 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1205810555 1.93E-06 NA mr1035 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
vg1205810555 NA 5.10E-06 mr1277 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
vg1205810555 3.55E-06 4.71E-06 mr1346 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
vg1205810555 2.14E-06 2.14E-06 mr1442 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
vg1205810555 3.80E-06 3.75E-06 mr1456 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
vg1205810555 7.47E-06 NA mr1626 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
vg1205810555 1.66E-06 NA mr1705 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
vg1205810555 3.61E-07 8.98E-07 mr1803 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
vg1205810555 2.47E-06 NA mr1965 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
vg1205810555 NA 8.19E-06 mr1277_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