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Detailed information for vg1216321299:

Variant ID: vg1216321299 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16321299
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTCGATTTCCAAAAAAAACTTGTGAAAAAGATTGAGTGGATTTGATGAGTAGAGATGGGGGGGAGAGAGGGGAGAAGGGCTTCTCTGCGTGCTCGGGC[T/C]
CCTAAGTTGGCGAAAATGAGTGGGGGAGGAGAAAGGAGGTGGGGCCCGCACGGGTTAAGGGCGCGGCCCACCCAGGGGGAGTGCGGCAGCCTTGCTAGCA

Reverse complement sequence

TGCTAGCAAGGCTGCCGCACTCCCCCTGGGTGGGCCGCGCCCTTAACCCGTGCGGGCCCCACCTCCTTTCTCCTCCCCCACTCATTTTCGCCAACTTAGG[A/G]
GCCCGAGCACGCAGAGAAGCCCTTCTCCCCTCTCTCCCCCCCATCTCTACTCATCAAATCCACTCAATCTTTTTCACAAGTTTTTTTTGGAAATCGAAGA

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 78.10% 1.80% 2.77% 17.39% NA
All Indica  2759 82.90% 0.40% 0.87% 15.84% NA
All Japonica  1512 69.40% 4.70% 6.02% 19.91% NA
Aus  269 77.70% 0.00% 1.86% 20.45% NA
Indica I  595 91.60% 0.00% 0.17% 8.24% NA
Indica II  465 58.50% 2.40% 3.66% 35.48% NA
Indica III  913 90.80% 0.00% 0.11% 9.09% NA
Indica Intermediate  786 81.40% 0.10% 0.64% 17.81% NA
Temperate Japonica  767 96.10% 0.00% 0.39% 3.52% NA
Tropical Japonica  504 22.40% 13.50% 16.07% 48.02% NA
Japonica Intermediate  241 82.60% 1.20% 2.90% 13.28% NA
VI/Aromatic  96 77.10% 0.00% 2.08% 20.83% NA
Intermediate  90 78.90% 1.10% 10.00% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216321299 T -> C LOC_Os12g27680-LOC_Os12g27690 intergenic_region ; MODIFIER silent_mutation Average:45.868; most accessible tissue: Minghui63 young leaf, score: 64.378 N N N N
vg1216321299 T -> DEL N N silent_mutation Average:45.868; most accessible tissue: Minghui63 young leaf, score: 64.378 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216321299 NA 2.41E-06 mr1036 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
vg1216321299 5.70E-06 5.70E-06 mr1131 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
vg1216321299 2.05E-06 NA mr1156 Jap_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
vg1216321299 1.36E-06 NA mr1236 Jap_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
vg1216321299 NA 8.64E-08 mr1382 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
vg1216321299 7.08E-06 NA mr1386 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
vg1216321299 NA 1.66E-06 mr1414 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
vg1216321299 4.02E-06 NA mr1491 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
vg1216321299 1.23E-07 3.20E-11 mr1696 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
vg1216321299 NA 3.39E-09 mr1696 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
vg1216321299 NA 2.76E-06 mr1697 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
vg1216321299 3.18E-06 NA mr1022_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
vg1216321299 2.16E-06 NA mr1023_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
vg1216321299 1.39E-06 NA mr1055_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
vg1216321299 5.92E-07 NA mr1079_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
vg1216321299 6.34E-06 NA mr1132_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
vg1216321299 2.17E-07 NA mr1390_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
vg1216321299 4.39E-06 NA mr1489_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