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Detailed information for vg0319043512:

Variant ID: vg0319043512 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 19043512
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTGTGAGCATTACTCGTTTGTGTCTTCTCTTGAACCTTTAAGGGTGGAAGAATCTTTTAATGATCCGGATTGGGTGATGGCGATGCAAGAGGAGCTGAA[C/T]
AATTTCACCCGGAATGAAGTGTGGACTTTGGTGGAGCGACCTCGGCAAAACGTGATTGGCATGAAGTGGATCTTCCGCAACAAGCAAGACGAGGCCGGGG

Reverse complement sequence

CCCCGGCCTCGTCTTGCTTGTTGCGGAAGATCCACTTCATGCCAATCACGTTTTGCCGAGGTCGCTCCACCAAAGTCCACACTTCATTCCGGGTGAAATT[G/A]
TTCAGCTCCTCTTGCATCGCCATCACCCAATCCGGATCATTAAAAGATTCTTCCACCCTTAAAGGTTCAAGAGAAGACACAAACGAGTAATGCTCACAAA

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 53.00% 33.00% 0.78% 13.20% NA
All Indica  2759 78.70% 4.30% 1.12% 15.84% NA
All Japonica  1512 1.90% 86.20% 0.26% 11.64% NA
Aus  269 89.20% 10.00% 0.00% 0.74% NA
Indica I  595 93.10% 3.50% 0.67% 2.69% NA
Indica II  465 74.40% 5.20% 1.51% 18.92% NA
Indica III  913 69.40% 1.80% 1.86% 26.94% NA
Indica Intermediate  786 81.20% 7.40% 0.38% 11.07% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 5.00% 66.30% 0.40% 28.37% NA
Japonica Intermediate  241 0.80% 84.60% 0.83% 13.69% NA
VI/Aromatic  96 25.00% 71.90% 0.00% 3.12% NA
Intermediate  90 46.70% 44.40% 2.22% 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
vg0319043512 C -> T LOC_Os03g33300.1 synonymous_variant ; p.Asn8Asn; LOW synonymous_codon Average:24.426; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 N N N N
vg0319043512 C -> DEL LOC_Os03g33300.1 N frameshift_variant Average:24.426; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0319043512 NA 7.32E-08 mr1136 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
vg0319043512 NA 5.38E-07 mr1227 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
vg0319043512 NA 8.94E-06 mr1227 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
vg0319043512 7.64E-07 3.39E-12 mr1718 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
vg0319043512 2.67E-08 NA mr1750 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
vg0319043512 2.98E-10 1.52E-18 mr1750 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
vg0319043512 3.30E-06 3.30E-06 mr1987 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
vg0319043512 NA 2.78E-08 mr1136_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
vg0319043512 8.70E-06 8.70E-06 mr1448_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
vg0319043512 NA 6.39E-12 mr1718_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
vg0319043512 3.29E-06 1.86E-19 mr1750_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