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Detailed information for vg1202381362:

Variant ID: vg1202381362 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2381362
Reference Allele: CAlternative Allele: T
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: 268. )

Flanking Sequence (100 bp) in Reference Genome:


ATCAGCAAAGACTAGGCCATCATTAGATGCGCTTATGGATTTGTACTTTGAAGCAACAGTCTGATCCACCTTATGTGTATCCCATTCACCAATAGCCTGG[C/T]
AACAATTTAAAAAAAAAAGAAAACTAGCAAGTTTTTTAGGATGAAGATACGTCAGAACAAGAAAAGGAAACCACGGATAACTTATCGAAGATCATTGTAG

Reverse complement sequence

CTACAATGATCTTCGATAAGTTATCCGTGGTTTCCTTTTCTTGTTCTGACGTATCTTCATCCTAAAAAACTTGCTAGTTTTCTTTTTTTTTTAAATTGTT[G/A]
CCAGGCTATTGGTGAATGGGATACACATAAGGTGGATCAGACTGTTGCTTCAAAGTACAAATCCATAAGCGCATCTAATGATGGCCTAGTCTTTGCTGAT

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 95.80% 3.30% 0.93% 0.00% NA
All Indica  2759 99.20% 0.40% 0.40% 0.00% NA
All Japonica  1512 89.00% 8.90% 2.18% 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 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.20% 0.10% 0.66% 0.00% NA
Indica Intermediate  786 98.50% 0.90% 0.64% 0.00% NA
Temperate Japonica  767 98.80% 0.30% 0.91% 0.00% NA
Tropical Japonica  504 72.80% 23.40% 3.77% 0.00% NA
Japonica Intermediate  241 91.30% 5.80% 2.90% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg1202381362 C -> T LOC_Os12g05310.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:36.767; most accessible tissue: Callus, score: 61.735 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202381362 NA 3.75E-06 mr1096 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
vg1202381362 1.71E-06 5.02E-08 mr1068_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
vg1202381362 NA 3.59E-06 mr1078_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
vg1202381362 7.05E-07 2.11E-08 mr1090_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
vg1202381362 NA 2.72E-06 mr1094_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
vg1202381362 NA 1.13E-06 mr1096_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
vg1202381362 NA 1.16E-06 mr1110_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
vg1202381362 NA 5.09E-07 mr1121_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
vg1202381362 NA 2.28E-06 mr1211_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