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Detailed information for vg0617644367:

Variant ID: vg0617644367 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 17644367
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.51, G: 0.49, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGTCTACTCCACTCGTTGTGTGAGCGCCTAAAGCCGGAAAGCCGTTTCGGTTATATATTGCCTCCGAAGACAAAGTCATTGGTGCCGTTTTGACGCAA[C/G]
AGGAAGATGGCAAGGAATATATCATTACATATTTGAGCCGCCGTCTTTTGGATGCCGAAACGAGGTATGTCTTTATAGAGAGACTTTGTCTATGCTTATA

Reverse complement sequence

TATAAGCATAGACAAAGTCTCTCTATAAAGACATACCTCGTTTCGGCATCCAAAAGACGGCGGCTCAAATATGTAATGATATATTCCTTGCCATCTTCCT[G/C]
TTGCGTCAAAACGGCACCAATGACTTTGTCTTCGGAGGCAATATATAACCGAAACGGCTTTCCGGCTTTAGGCGCTCACACAACGAGTGGAGTAGACAAA

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 46.20% 5.60% 20.31% 27.93% NA
All Indica  2759 18.70% 6.90% 29.10% 45.34% NA
All Japonica  1512 97.20% 0.40% 0.66% 1.79% NA
Aus  269 26.00% 22.70% 44.98% 6.32% NA
Indica I  595 23.70% 9.10% 28.57% 38.66% NA
Indica II  465 12.70% 5.80% 26.45% 55.05% NA
Indica III  913 16.20% 6.70% 29.35% 47.75% NA
Indica Intermediate  786 21.20% 6.10% 30.79% 41.86% NA
Temperate Japonica  767 95.80% 0.40% 0.78% 3.00% NA
Tropical Japonica  504 99.00% 0.20% 0.40% 0.40% NA
Japonica Intermediate  241 97.50% 0.80% 0.83% 0.83% NA
VI/Aromatic  96 77.10% 4.20% 15.62% 3.12% NA
Intermediate  90 60.00% 3.30% 12.22% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0617644367 C -> G LOC_Os06g30510.1 intron_variant ; MODIFIER silent_mutation Average:10.648; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N
vg0617644367 C -> DEL N N silent_mutation Average:10.648; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0617644367 NA 4.03E-07 mr1033 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
vg0617644367 NA 1.80E-06 mr1155 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
vg0617644367 NA 1.20E-06 mr1526 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
vg0617644367 3.85E-07 3.85E-07 mr1529 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
vg0617644367 NA 6.39E-06 mr1096_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
vg0617644367 NA 2.38E-07 mr1111_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