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Detailed information for vg0224207984:

Variant ID: vg0224207984 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24207984
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, C: 0.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTGTGGTTATTTGCGGGTACGGAACGAAATGCGGGTACGTGGAAGAGACGGAATTAATCATGGAAATGATTTCACCATGAAAATGGCACAAGGCAGTG[A/C]
TCACATTTGTGTCTTATGCCTGATAACGACCGGGGCCTCCTTTGGATTTGGATGAACTTCTGTAAAAATCCTGTAAAATTCTTATAAAAATTTGGTGAAT

Reverse complement sequence

ATTCACCAAATTTTTATAAGAATTTTACAGGATTTTTACAGAAGTTCATCCAAATCCAAAGGAGGCCCCGGTCGTTATCAGGCATAAGACACAAATGTGA[T/G]
CACTGCCTTGTGCCATTTTCATGGTGAAATCATTTCCATGATTAATTCCGTCTCTTCCACGTACCCGCATTTCGTTCCGTACCCGCAAATAACCACAAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.40% 10.30% 0.32% 0.00% NA
All Indica  2759 91.00% 8.80% 0.11% 0.00% NA
All Japonica  1512 86.90% 12.40% 0.66% 0.00% NA
Aus  269 93.70% 6.30% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 88.20% 11.80% 0.00% 0.00% NA
Indica III  913 86.90% 13.00% 0.11% 0.00% NA
Indica Intermediate  786 91.10% 8.70% 0.25% 0.00% NA
Temperate Japonica  767 85.70% 13.20% 1.17% 0.00% NA
Tropical Japonica  504 97.40% 2.60% 0.00% 0.00% NA
Japonica Intermediate  241 68.90% 30.70% 0.41% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 81.10% 16.70% 2.22% 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
vg0224207984 A -> C LOC_Os02g40000-LOC_Os02g40010 intergenic_region ; MODIFIER silent_mutation Average:61.133; most accessible tissue: Minghui63 flower, score: 84.277 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224207984 2.63E-06 3.94E-08 mr1170 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
vg0224207984 1.81E-06 1.81E-06 mr1373 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
vg0224207984 NA 4.24E-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
vg0224207984 5.07E-06 1.77E-07 mr1445 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
vg0224207984 5.69E-06 6.50E-06 mr1513 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
vg0224207984 1.86E-06 NA mr1055_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
vg0224207984 6.74E-07 NA mr1079_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
vg0224207984 5.51E-08 NA mr1132_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
vg0224207984 3.90E-07 NA mr1178_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
vg0224207984 3.56E-08 NA mr1390_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
vg0224207984 1.74E-06 NA mr1489_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
vg0224207984 6.72E-07 NA mr1490_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