\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1218067516:

Variant ID: vg1218067516 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18067516
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, T: 0.07, others allele: 0.00, population size: 27. )

Flanking Sequence (100 bp) in Reference Genome:


CACAATAGTTATACCTCATTTACACCCCACTTACATATATAATTGGTATGTAATTTTCGAATTTACATATGTAATTTTAGTACTTACATATATAATTTTG[T/A]
GACTTACATTGTAAATACACTAAAATTACATATGTAATTTAGGGACTTACAGTGTAAATAAATACCGACTATTTTTTGATGAAAAATATGGCGCCATATA

Reverse complement sequence

TATATGGCGCCATATTTTTCATCAAAAAATAGTCGGTATTTATTTACACTGTAAGTCCCTAAATTACATATGTAATTTTAGTGTATTTACAATGTAAGTC[A/T]
CAAAATTATATATGTAAGTACTAAAATTACATATGTAAATTCGAAAATTACATACCAATTATATATGTAAGTGGGGTGTAAATGAGGTATAACTATTGTG

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 25.80% 14.20% 1.16% 58.80% NA
All Indica  2759 40.50% 1.40% 1.63% 56.43% NA
All Japonica  1512 5.40% 36.00% 0.20% 58.47% NA
Aus  269 1.90% 23.40% 0.74% 73.98% NA
Indica I  595 81.00% 1.00% 0.34% 17.65% NA
Indica II  465 15.70% 2.40% 0.22% 81.72% NA
Indica III  913 27.60% 0.40% 2.96% 69.00% NA
Indica Intermediate  786 39.60% 2.30% 1.91% 56.23% NA
Temperate Japonica  767 0.40% 63.40% 0.26% 35.98% NA
Tropical Japonica  504 4.40% 1.80% 0.20% 93.65% NA
Japonica Intermediate  241 23.20% 20.30% 0.00% 56.43% NA
VI/Aromatic  96 0.00% 3.10% 3.12% 93.75% NA
Intermediate  90 16.70% 26.70% 2.22% 54.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218067516 T -> DEL N N silent_mutation Average:28.314; most accessible tissue: Callus, score: 52.127 N N N N
vg1218067516 T -> A LOC_Os12g30130.1 upstream_gene_variant ; 1051.0bp to feature; MODIFIER silent_mutation Average:28.314; most accessible tissue: Callus, score: 52.127 N N N N
vg1218067516 T -> A LOC_Os12g30120-LOC_Os12g30130 intergenic_region ; MODIFIER silent_mutation Average:28.314; most accessible tissue: Callus, score: 52.127 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218067516 NA 5.63E-09 mr1023 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
vg1218067516 NA 1.92E-08 mr1163 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
vg1218067516 NA 6.41E-06 mr1280 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
vg1218067516 NA 1.22E-09 mr1486 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
vg1218067516 NA 9.38E-13 mr1546 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
vg1218067516 NA 2.98E-06 mr1548 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
vg1218067516 NA 2.79E-07 mr1617 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
vg1218067516 3.66E-06 3.01E-12 mr1624 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
vg1218067516 NA 3.53E-06 mr1624 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
vg1218067516 NA 3.19E-06 mr1937 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
vg1218067516 NA 4.52E-13 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
vg1218067516 NA 9.58E-12 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
vg1218067516 NA 8.35E-13 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
vg1218067516 4.82E-07 NA mr1458_2 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
vg1218067516 4.48E-06 3.82E-07 mr1458_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
vg1218067516 NA 2.52E-09 mr1486_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
vg1218067516 NA 2.01E-06 mr1577_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
vg1218067516 NA 9.66E-07 mr1792_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
vg1218067516 NA 6.47E-07 mr1803_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