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Detailed information for vg0308150228:

Variant ID: vg0308150228 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 8150228
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATATTGGGATTTGATAAAGCAGAGATATTTTAGGTTTTTAGTTTTGTATTGGTATGTATTAAATGGATGACAAATGAATTTACTTTAGAACGGAGGTAG[T/C]
AAAAAAGATGAACAATACTTGATTTGAGTACCACCACCATGCACCCAATGTAGTATACTCTCCTACTTGTAGCTGTTTTCCTGCGATCAGGATCCTCTAC

Reverse complement sequence

GTAGAGGATCCTGATCGCAGGAAAACAGCTACAAGTAGGAGAGTATACTACATTGGGTGCATGGTGGTGGTACTCAAATCAAGTATTGTTCATCTTTTTT[A/G]
CTACCTCCGTTCTAAAGTAAATTCATTTGTCATCCATTTAATACATACCAATACAAAACTAAAAACCTAAAATATCTCTGCTTTATCAAATCCCAATATA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.80% 11.10% 0.04% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 66.00% 33.90% 0.13% 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 99.80% 0.20% 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 73.00% 27.00% 0.00% 0.00% NA
Tropical Japonica  504 72.60% 27.20% 0.20% 0.00% NA
Japonica Intermediate  241 29.90% 69.70% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0308150228 T -> C LOC_Os03g14950.1 upstream_gene_variant ; 2316.0bp to feature; MODIFIER silent_mutation Average:68.456; most accessible tissue: Callus, score: 83.585 N N N N
vg0308150228 T -> C LOC_Os03g14940-LOC_Os03g14950 intergenic_region ; MODIFIER silent_mutation Average:68.456; most accessible tissue: Callus, score: 83.585 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0308150228 2.77E-06 NA mr1617 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
vg0308150228 6.62E-08 2.81E-10 mr1712 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
vg0308150228 1.86E-06 2.87E-06 mr1712 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
vg0308150228 9.49E-06 NA mr1718 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
vg0308150228 NA 7.20E-07 mr1559_2 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
vg0308150228 NA 1.52E-07 mr1691_2 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