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Detailed information for vg1210706721:

Variant ID: vg1210706721 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 10706721
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTTTCCTTTTTAAAAAAAACGACACCCTATAAAACAAGCTGAGACGAGAGAGTCGTTTTTTCTCTTTTAGTGCATGGGGCGGGCGCCGAGATAAATTAC[C/T]
GCGTGAGAGGTGAGGGGGGTGAGTGGATAAGGACGCCCCCCCCCCCCCCTCTTCACCTCCTCTCACGGTCTCACCCTCTACCTCTCACTCCCTCTTGTCC

Reverse complement sequence

GGACAAGAGGGAGTGAGAGGTAGAGGGTGAGACCGTGAGAGGAGGTGAAGAGGGGGGGGGGGGGGCGTCCTTATCCACTCACCCCCCTCACCTCTCACGC[G/A]
GTAATTTATCTCGGCGCCCGCCCCATGCACTAAAAGAGAAAAAACGACTCTCTCGTCTCAGCTTGTTTTATAGGGTGTCGTTTTTTTTAAAAAGGAAACT

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 99.20% 0.80% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 97.60% 2.40% 0.00% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 95.40% 4.60% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1210706721 C -> T LOC_Os12g18510.1 upstream_gene_variant ; 2702.0bp to feature; MODIFIER silent_mutation Average:62.67; most accessible tissue: Zhenshan97 young leaf, score: 79.507 N N N N
vg1210706721 C -> T LOC_Os12g18520.1 upstream_gene_variant ; 3243.0bp to feature; MODIFIER silent_mutation Average:62.67; most accessible tissue: Zhenshan97 young leaf, score: 79.507 N N N N
vg1210706721 C -> T LOC_Os12g18510-LOC_Os12g18520 intergenic_region ; MODIFIER silent_mutation Average:62.67; most accessible tissue: Zhenshan97 young leaf, score: 79.507 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1210706721 NA 4.06E-07 mr1354 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
vg1210706721 NA 3.49E-08 mr1829 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
vg1210706721 NA 2.56E-07 mr1354_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
vg1210706721 8.56E-07 8.56E-07 mr1587_2 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
vg1210706721 NA 6.29E-07 mr1792_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
vg1210706721 NA 1.23E-06 mr1803_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
vg1210706721 NA 9.68E-09 mr1829_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
vg1210706721 NA 7.76E-06 mr1842_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
vg1210706721 NA 4.08E-08 mr1902_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