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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0529371054:

Variant ID: vg0529371054 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 29371054
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GTATCTCATGAGCCTGTTCGACTACAGAACGGTTGTTAGCCATCTTGTAGTCATGAAACTGCTCCATGATATACAGATCATTGCTAGCATCAGTAGCACC[A/G]
AATTTAGTATTCAGTGCATCCCACAATTCCTTAGCGTCGGTCATATGCATATACACCTCGACAAGACGATCGCCAAGCACGCTAAGAATGCATCCCATAA

Reverse complement sequence

TTATGGGATGCATTCTTAGCGTGCTTGGCGATCGTCTTGTCGAGGTGTATATGCATATGACCGACGCTAAGGAATTGTGGGATGCACTGAATACTAAATT[T/C]
GGTGCTACTGATGCTAGCAATGATCTGTATATCATGGAGCAGTTTCATGACTACAAGATGGCTAACAACCGTTCTGTAGTCGAACAGGCTCATGAGATAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.50% 36.20% 0.25% 0.00% NA
All Indica  2759 94.30% 5.40% 0.36% 0.00% NA
All Japonica  1512 4.80% 95.20% 0.00% 0.00% NA
Aus  269 97.00% 2.60% 0.37% 0.00% NA
Indica I  595 98.20% 1.50% 0.34% 0.00% NA
Indica II  465 83.40% 16.10% 0.43% 0.00% NA
Indica III  913 97.70% 1.90% 0.44% 0.00% NA
Indica Intermediate  786 93.80% 6.00% 0.25% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 13.10% 86.90% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 57.80% 41.10% 1.11% 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
vg0529371054 A -> G LOC_Os05g51200.1 synonymous_variant ; p.Phe94Phe; LOW synonymous_codon Average:18.383; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0529371054 2.02E-06 NA mr1161 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
vg0529371054 NA 2.36E-22 mr1548 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
vg0529371054 NA 2.37E-20 mr1588 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
vg0529371054 NA 9.61E-15 mr1162_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
vg0529371054 NA 3.50E-07 mr1478_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
vg0529371054 NA 1.09E-28 mr1588_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
vg0529371054 NA 2.60E-08 mr1588_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
vg0529371054 NA 8.70E-17 mr1712_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
vg0529371054 NA 2.35E-07 mr1749_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
vg0529371054 NA 1.11E-10 mr1893_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