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Detailed information for vg1215163870:

Variant ID: vg1215163870 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15163870
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


ATATATATATATATATATATATATATATATATATATGTATTTAAACATATATATATGCATAGTATATCAGTACAGTCAGCAAGCAACACAACAAAATAAT[A/T]
AAAAAGAAAAAATGTCTTTAGTCCCGAGACTAAAGATGGCTGAGCCACATACTATCTTTAGTTCTAGATTCTCCCTTCCGGTTTATAACCCGGGACTAAA

Reverse complement sequence

TTTAGTCCCGGGTTATAAACCGGAAGGGAGAATCTAGAACTAAAGATAGTATGTGGCTCAGCCATCTTTAGTCTCGGGACTAAAGACATTTTTTCTTTTT[T/A]
ATTATTTTGTTGTGTTGCTTGCTGACTGTACTGATATACTATGCATATATATATGTTTAAATACATATATATATATATATATATATATATATATATATAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 36.40% 24.10% 0.61% 38.85% NA
All Indica  2759 22.50% 32.90% 0.87% 43.71% NA
All Japonica  1512 68.80% 13.40% 0.07% 17.72% NA
Aus  269 6.30% 1.90% 0.37% 91.45% NA
Indica I  595 13.90% 23.00% 1.18% 61.85% NA
Indica II  465 25.80% 55.70% 0.86% 17.63% NA
Indica III  913 26.40% 25.40% 0.00% 48.19% NA
Indica Intermediate  786 22.50% 35.60% 1.65% 40.20% NA
Temperate Japonica  767 88.90% 6.50% 0.00% 4.56% NA
Tropical Japonica  504 42.10% 22.20% 0.20% 35.52% NA
Japonica Intermediate  241 60.60% 17.00% 0.00% 22.41% NA
VI/Aromatic  96 2.10% 2.10% 2.08% 93.75% NA
Intermediate  90 45.60% 24.40% 1.11% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1215163870 A -> DEL N N silent_mutation Average:14.002; most accessible tissue: Callus, score: 47.919 N N N N
vg1215163870 A -> T LOC_Os12g26080-LOC_Os12g26090 intergenic_region ; MODIFIER silent_mutation Average:14.002; most accessible tissue: Callus, score: 47.919 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215163870 NA 7.64E-06 mr1136 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
vg1215163870 NA 1.76E-07 mr1188 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
vg1215163870 NA 3.24E-07 mr1280 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
vg1215163870 NA 1.49E-06 mr1298 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
vg1215163870 NA 3.96E-07 mr1308 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
vg1215163870 9.61E-06 9.61E-06 mr1544 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
vg1215163870 8.56E-06 6.76E-08 mr1579 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
vg1215163870 NA 3.62E-06 mr1603 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
vg1215163870 NA 1.58E-08 mr1188_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
vg1215163870 NA 5.38E-06 mr1633_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
vg1215163870 NA 1.08E-06 mr1653_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
vg1215163870 NA 9.76E-06 mr1830_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
vg1215163870 NA 3.49E-06 mr1887_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