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Detailed information for vg1012224371:

Variant ID: vg1012224371 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 12224371
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, G: 0.04, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


TCGACGCCATGAGGAGGAACGAGATCGACAAGGTCCCCGGCTGCAGCCTCATCGAGATCGACGGCGTTGTGCACGAATTCAAAGCAATCCCAGCAAATTC[C/G]
ATCCGATAAAAACTCAAGAAGATTCATCAAAGAACAGGTTATCCGATTGATCGATTGATCACTGTAGATAACAAGATTCATAGAACCACGGATGCAAGAT

Reverse complement sequence

ATCTTGCATCCGTGGTTCTATGAATCTTGTTATCTACAGTGATCAATCGATCAATCGGATAACCTGTTCTTTGATGAATCTTCTTGAGTTTTTATCGGAT[G/C]
GAATTTGCTGGGATTGCTTTGAATTCGTGCACAACGCCGTCGATCTCGATGAGGCTGCAGCCGGGGACCTTGTCGATCTCGTTCCTCCTCATGGCGTCGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 31.40% 17.80% 1.04% 49.83% NA
All Indica  2759 2.90% 28.60% 1.52% 67.02% NA
All Japonica  1512 89.40% 0.40% 0.07% 10.19% NA
Aus  269 2.20% 9.70% 1.49% 86.62% NA
Indica I  595 3.90% 7.20% 2.52% 86.39% NA
Indica II  465 3.40% 36.30% 1.29% 58.92% NA
Indica III  913 1.80% 33.60% 1.10% 63.53% NA
Indica Intermediate  786 3.10% 34.40% 1.40% 61.20% NA
Temperate Japonica  767 97.00% 0.30% 0.00% 2.74% NA
Tropical Japonica  504 81.70% 0.40% 0.20% 17.66% NA
Japonica Intermediate  241 80.90% 0.80% 0.00% 18.26% NA
VI/Aromatic  96 6.20% 3.10% 2.08% 88.54% NA
Intermediate  90 44.40% 17.80% 0.00% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1012224371 C -> G LOC_Os10g23830.1 synonymous_variant ; p.Ser155Ser; LOW synonymous_codon Average:27.003; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg1012224371 C -> DEL LOC_Os10g23830.1 N frameshift_variant Average:27.003; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1012224371 NA 1.79E-07 mr1157 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
vg1012224371 NA 4.99E-06 mr1157 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
vg1012224371 NA 2.31E-09 mr1328 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
vg1012224371 NA 6.91E-08 mr1328 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
vg1012224371 NA 9.15E-10 mr1446 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
vg1012224371 NA 1.45E-07 mr1446 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
vg1012224371 1.26E-06 2.34E-13 mr1446_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
vg1012224371 NA 4.50E-09 mr1446_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
vg1012224371 NA 7.60E-06 mr1567_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