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Detailed information for vg1017092925:

Variant ID: vg1017092925 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 17092925
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


CCGGAGGCCTCGCCTGTGTGTAGTTGGTTCTCCCGCTATCCCATTGAGTAAAATTCTGGATGATGCAGTCGATAGGAGAAGCACAATCCAATTTCTCCAG[T/C]
GCTGACTAAAGCCTCTGCACTGCAGCATTTCGACAAGGTATTCCCAAGATACCGAATCAAATGCCTTTGTTATGTCCAACTTGAAGAAGAGGGATGGTTT

Reverse complement sequence

AAACCATCCCTCTTCTTCAAGTTGGACATAACAAAGGCATTTGATTCGGTATCTTGGGAATACCTTGTCGAAATGCTGCAGTGCAGAGGCTTTAGTCAGC[A/G]
CTGGAGAAATTGGATTGTGCTTCTCCTATCGACTGCATCATCCAGAATTTTACTCAATGGGATAGCGGGAGAACCAACTACACACAGGCGAGGCCTCCGG

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 93.40% 4.80% 1.80% 0.00% NA
All Indica  2759 99.30% 0.60% 0.07% 0.00% NA
All Japonica  1512 81.10% 13.40% 5.49% 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 98.50% 1.10% 0.43% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 64.80% 25.40% 9.78% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 93.80% 3.30% 2.90% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg1017092925 T -> C LOC_Os10g32630.1 missense_variant ; p.His368Arg; MODERATE nonsynonymous_codon ; H368R Average:26.57; most accessible tissue: Minghui63 root, score: 36.81 possibly damaging -1.652 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1017092925 NA 8.51E-06 mr1354 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
vg1017092925 2.36E-06 NA mr1902 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
vg1017092925 NA 1.86E-08 mr1902 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
vg1017092925 NA 3.67E-08 mr1010_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
vg1017092925 NA 2.19E-07 mr1011_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
vg1017092925 NA 7.28E-06 mr1138_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
vg1017092925 4.86E-08 NA mr1354_2 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
vg1017092925 NA 3.72E-09 mr1354_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
vg1017092925 NA 3.80E-06 mr1902_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