\

Search for Variation information by Variation ID:

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

Detailed information for vg1215653080:

Variant ID: vg1215653080 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15653080
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTTTCTAAATCCTACTTTGCAAAACAGAAAGTTGTTCTATTCTAATTTTTCTTTTTCCTTTACTGTTAAGGGTATTAAATAGTTTCCTGAATTTAAGTG[G/A]
TTAGTCGGCACTGTACATCTATTATGGTATCGATTGAATCAAGATAGCACTAGTACTAGTCATCCCTCTTAATGGTGACACTGTACCGTGCCTGTATAGA

Reverse complement sequence

TCTATACAGGCACGGTACAGTGTCACCATTAAGAGGGATGACTAGTACTAGTGCTATCTTGATTCAATCGATACCATAATAGATGTACAGTGCCGACTAA[C/T]
CACTTAAATTCAGGAAACTATTTAATACCCTTAACAGTAAAGGAAAAAGAAAAATTAGAATAGAACAACTTTCTGTTTTGCAAAGTAGGATTTAGAAAAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 45.90% 0.10% 6.56% 47.44% NA
All Indica  2759 20.60% 0.10% 8.63% 70.68% NA
All Japonica  1512 89.20% 0.00% 0.46% 10.38% NA
Aus  269 46.50% 0.40% 17.84% 35.32% NA
Indica I  595 12.40% 0.30% 3.70% 83.53% NA
Indica II  465 47.30% 0.00% 9.46% 43.23% NA
Indica III  913 9.90% 0.00% 11.94% 78.20% NA
Indica Intermediate  786 23.30% 0.30% 8.02% 68.45% NA
Temperate Japonica  767 96.00% 0.00% 0.13% 3.91% NA
Tropical Japonica  504 80.20% 0.00% 0.99% 18.85% NA
Japonica Intermediate  241 86.30% 0.00% 0.41% 13.28% NA
VI/Aromatic  96 70.80% 0.00% 11.46% 17.71% NA
Intermediate  90 67.80% 0.00% 6.67% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1215653080 G -> DEL N N silent_mutation Average:19.561; most accessible tissue: Minghui63 flag leaf, score: 38.911 N N N N
vg1215653080 G -> A LOC_Os12g26710.1 intron_variant ; MODIFIER silent_mutation Average:19.561; most accessible tissue: Minghui63 flag leaf, score: 38.911 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215653080 NA 7.41E-10 mr1016 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
vg1215653080 NA 1.12E-10 mr1017 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
vg1215653080 NA 3.31E-06 mr1156 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
vg1215653080 1.08E-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
vg1215653080 2.34E-08 2.25E-14 mr1023_2 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
vg1215653080 NA 7.95E-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
vg1215653080 NA 5.85E-12 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
vg1215653080 NA 4.15E-13 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
vg1215653080 6.66E-06 6.42E-10 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
vg1215653080 NA 1.50E-12 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