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Detailed information for vg0121870570:

Variant ID: vg0121870570 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 21870570
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


TGATAAACAAAAACAACGTTCTGAGGACCAGAGGGACAAGGCTTAGGCTTGATCGAGGGTGATGAGGGTCGTTCAGTTTCATGATGATGGGAAATAGGTT[C/T]
AGAAGAAACGAACGAAGATACAAAAATCACCTCCTCGAACGGTTCATGCTTGGGATGAGCCTTCGTTTTGCTGAAATGATTCAGGGTGTTTCCATAATCT

Reverse complement sequence

AGATTATGGAAACACCCTGAATCATTTCAGCAAAACGAAGGCTCATCCCAAGCATGAACCGTTCGAGGAGGTGATTTTTGTATCTTCGTTCGTTTCTTCT[G/A]
AACCTATTTCCCATCATCATGAAACTGAACGACCCTCATCACCCTCGATCAAGCCTAAGCCTTGTCCCTCTGGTCCTCAGAACGTTGTTTTTGTTTATCA

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 59.50% 8.50% 15.47% 16.53% NA
All Indica  2759 36.60% 13.00% 22.83% 27.58% NA
All Japonica  1512 99.50% 0.10% 0.20% 0.26% NA
Aus  269 58.40% 13.00% 25.28% 3.35% NA
Indica I  595 11.10% 19.50% 36.64% 32.77% NA
Indica II  465 48.80% 10.10% 17.63% 23.44% NA
Indica III  913 36.60% 12.20% 19.17% 32.09% NA
Indica Intermediate  786 48.60% 10.80% 19.72% 20.87% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.20% 0.20% 0.40% NA
Japonica Intermediate  241 98.30% 0.00% 0.83% 0.83% NA
VI/Aromatic  96 76.00% 3.10% 19.79% 1.04% NA
Intermediate  90 77.80% 3.30% 12.22% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0121870570 C -> T LOC_Os01g38930.1 intron_variant ; MODIFIER silent_mutation Average:12.545; most accessible tissue: Callus, score: 46.251 N N N N
vg0121870570 C -> DEL N N silent_mutation Average:12.545; most accessible tissue: Callus, score: 46.251 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0121870570 NA 1.19E-18 mr1077 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
vg0121870570 NA 4.55E-06 mr1343 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
vg0121870570 NA 1.12E-13 mr1655 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
vg0121870570 NA 6.13E-21 mr1698 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
vg0121870570 NA 9.34E-07 mr1717 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
vg0121870570 NA 3.13E-06 mr1748 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
vg0121870570 NA 9.84E-10 mr1770 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
vg0121870570 NA 5.28E-07 mr1785 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
vg0121870570 NA 4.94E-06 mr1795 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
vg0121870570 NA 2.60E-07 mr1962 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