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Detailed information for vg1217990202:

Variant ID: vg1217990202 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17990202
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTCTCCAAAATTTATGTAAGGCCTGGTTTAGTTCCCAACTTTTTCTTCAAACTTCTAACTTTTCTATCACATCAAAACTTTCCTATACACACAAACTTT[C/T]
AACTTTTTCATCACATCGTTTCAATTTCAATCAAACTTTTAATTTTGACGTGAACTAAATACACCCTAACTTTCGTTTGAATCAACCAGGGATTAATTAA

Reverse complement sequence

TTAATTAATCCCTGGTTGATTCAAACGAAAGTTAGGGTGTATTTAGTTCACGTCAAAATTAAAAGTTTGATTGAAATTGAAACGATGTGATGAAAAAGTT[G/A]
AAAGTTTGTGTGTATAGGAAAGTTTTGATGTGATAGAAAAGTTAGAAGTTTGAAGAAAAAGTTGGGAACTAAACCAGGCCTTACATAAATTTTGGAGAAT

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 90.20% 9.70% 0.04% 0.00% NA
All Indica  2759 93.40% 6.60% 0.04% 0.00% NA
All Japonica  1512 89.60% 10.40% 0.00% 0.00% NA
Aus  269 69.50% 30.10% 0.37% 0.00% NA
Indica I  595 94.50% 5.50% 0.00% 0.00% NA
Indica II  465 82.60% 17.40% 0.00% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 95.20% 4.70% 0.13% 0.00% NA
Temperate Japonica  767 86.40% 13.60% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 81.30% 18.70% 0.00% 0.00% NA
VI/Aromatic  96 65.60% 34.40% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1217990202 C -> T LOC_Os12g30050.1 upstream_gene_variant ; 4122.0bp to feature; MODIFIER silent_mutation Average:37.371; most accessible tissue: Callus, score: 56.927 N N N N
vg1217990202 C -> T LOC_Os12g30040-LOC_Os12g30050 intergenic_region ; MODIFIER silent_mutation Average:37.371; most accessible tissue: Callus, score: 56.927 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217990202 NA 4.48E-06 mr1188 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
vg1217990202 3.27E-06 3.27E-06 mr1191 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
vg1217990202 NA 3.43E-07 mr1458 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
vg1217990202 NA 7.04E-08 mr1570 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
vg1217990202 NA 1.49E-08 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