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Detailed information for vg1218290915:

Variant ID: vg1218290915 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18290915
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGAGCTGTCTTGCCTTTGTGATATGGAAGTGGGAAGCAGCGGCAAAGAAGTGGCCATATACTTTATTAGTTGAGCACAACTTAGGAAACTATTCTAATC[C/T]
CTCGAGAGGGGATGTTCCCTTCTTTACTTAAAAACCATATAAACGGTTATGAAAAATTCTGAAAAAATTTGGCAACATTCATACAACACATATATACAAC

Reverse complement sequence

GTTGTATATATGTGTTGTATGAATGTTGCCAAATTTTTTCAGAATTTTTCATAACCGTTTATATGGTTTTTAAGTAAAGAAGGGAACATCCCCTCTCGAG[G/A]
GATTAGAATAGTTTCCTAAGTTGTGCTCAACTAATAAAGTATATGGCCACTTCTTTGCCGCTGCTTCCCACTTCCATATCACAAAGGCAAGACAGCTCAA

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 69.30% 30.60% 0.11% 0.00% NA
All Indica  2759 75.20% 24.70% 0.11% 0.00% NA
All Japonica  1512 54.90% 45.00% 0.07% 0.00% NA
Aus  269 81.40% 18.60% 0.00% 0.00% NA
Indica I  595 59.00% 40.80% 0.17% 0.00% NA
Indica II  465 70.50% 29.50% 0.00% 0.00% NA
Indica III  913 85.90% 14.10% 0.00% 0.00% NA
Indica Intermediate  786 77.90% 21.90% 0.25% 0.00% NA
Temperate Japonica  767 70.40% 29.60% 0.00% 0.00% NA
Tropical Japonica  504 27.60% 72.40% 0.00% 0.00% NA
Japonica Intermediate  241 62.70% 36.90% 0.41% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 71.10% 27.80% 1.11% 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
vg1218290915 C -> T LOC_Os12g30460.1 intron_variant ; MODIFIER silent_mutation Average:57.922; most accessible tissue: Zhenshan97 flower, score: 76.106 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218290915 NA 5.53E-06 mr1026 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
vg1218290915 NA 7.95E-09 mr1137 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
vg1218290915 NA 1.29E-06 mr1163 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
vg1218290915 NA 7.49E-06 mr1171 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
vg1218290915 NA 2.54E-08 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
vg1218290915 NA 3.45E-06 mr1492 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
vg1218290915 NA 9.53E-08 mr1617 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
vg1218290915 NA 8.33E-06 mr1686 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
vg1218290915 NA 1.12E-09 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
vg1218290915 NA 5.54E-08 mr1790_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
vg1218290915 NA 7.01E-06 mr1968_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