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Detailed information for vg0618007086:

Variant ID: vg0618007086 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 18007086
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


CAACTCTTTTTATTTAAAACATCTTACTTTTATAGATATTGTTTGTCAAAGTAGCATCTCGGAGACCGTGTCAGACTCTAAAAATGCTTATATTTTGGAA[T/C]
GAAGGGAGTAAATAATTCATAGATGCACGCTCACTCAAAATCATTCTTTCTAGGGGGAGACCTGTTCTGTGTCATCTCTTGGGAAGCATTAATGTTCTAT

Reverse complement sequence

ATAGAACATTAATGCTTCCCAAGAGATGACACAGAACAGGTCTCCCCCTAGAAAGAATGATTTTGAGTGAGCGTGCATCTATGAATTATTTACTCCCTTC[A/G]
TTCCAAAATATAAGCATTTTTAGAGTCTGACACGGTCTCCGAGATGCTACTTTGACAAACAATATCTATAAAAGTAAGATGTTTTAAATAAAAAGAGTTG

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 80.50% 19.50% 0.02% 0.00% NA
All Indica  2759 98.00% 2.00% 0.00% 0.00% NA
All Japonica  1512 44.10% 55.80% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.70% 0.00% 0.00% NA
Temperate Japonica  767 54.50% 45.40% 0.13% 0.00% NA
Tropical Japonica  504 19.60% 80.40% 0.00% 0.00% NA
Japonica Intermediate  241 62.20% 37.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 73.30% 26.70% 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
vg0618007086 T -> C LOC_Os06g30950.1 intron_variant ; MODIFIER silent_mutation Average:42.985; most accessible tissue: Minghui63 flower, score: 51.629 N N N N
vg0618007086 T -> C LOC_Os06g30950.2 intron_variant ; MODIFIER silent_mutation Average:42.985; most accessible tissue: Minghui63 flower, score: 51.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0618007086 NA 6.48E-06 mr1071 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
vg0618007086 NA 9.70E-06 mr1140 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
vg0618007086 NA 2.15E-07 mr1354 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
vg0618007086 NA 6.79E-21 mr1518 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
vg0618007086 NA 2.57E-06 mr1518 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
vg0618007086 NA 1.01E-25 mr1676 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
vg0618007086 NA 3.73E-08 mr1676 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
vg0618007086 2.83E-06 5.98E-09 mr1707 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
vg0618007086 NA 1.41E-06 mr1993 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
vg0618007086 NA 5.23E-09 mr1354_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
vg0618007086 NA 9.20E-06 mr1707_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