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Detailed information for vg1019872900:

Variant ID: vg1019872900 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 19872900
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


CCTTGATGCGTACAGCGGTCGGAGCTTCACTATTCCCTCGACCTCCACAGCACGCCGCACAGTTAGCTCTCGGGCTCTGTGTGATCCTAGCCGCTCCGCC[A/G]
CCACTCACGGTTGTCGGAGTAACACTTCCGCCCCACTAAACCCACACAAACCTCCTATCCCTCTAACCGTTATGCTGTCTGTTGACACCGGCTAGAGAAG

Reverse complement sequence

CTTCTCTAGCCGGTGTCAACAGACAGCATAACGGTTAGAGGGATAGGAGGTTTGTGTGGGTTTAGTGGGGCGGAAGTGTTACTCCGACAACCGTGAGTGG[T/C]
GGCGGAGCGGCTAGGATCACACAGAGCCCGAGAGCTAACTGTGCGGCGTGCTGTGGAGGTCGAGGGAATAGTGAAGCTCCGACCGCTGTACGCATCAAGG

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 28.80% 23.30% 8.70% 39.21% NA
All Indica  2759 34.40% 2.10% 8.74% 54.80% NA
All Japonica  1512 12.80% 66.70% 7.94% 12.63% NA
Aus  269 54.60% 0.70% 5.95% 38.66% NA
Indica I  595 7.70% 2.50% 10.08% 79.66% NA
Indica II  465 47.30% 1.70% 9.68% 41.29% NA
Indica III  913 44.70% 2.00% 7.12% 46.22% NA
Indica Intermediate  786 34.90% 2.20% 9.03% 53.94% NA
Temperate Japonica  767 0.50% 87.60% 7.04% 4.82% NA
Tropical Japonica  504 34.90% 27.60% 11.71% 25.79% NA
Japonica Intermediate  241 5.40% 81.70% 2.90% 9.96% NA
VI/Aromatic  96 49.00% 11.50% 16.67% 22.92% NA
Intermediate  90 31.10% 22.20% 20.00% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1019872900 A -> G LOC_Os10g37120-LOC_Os10g37160 intergenic_region ; MODIFIER silent_mutation Average:19.377; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg1019872900 A -> DEL N N silent_mutation Average:19.377; 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
vg1019872900 NA 5.79E-06 mr1096 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
vg1019872900 NA 1.13E-08 mr1261_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
vg1019872900 2.54E-06 2.54E-06 mr1299_2 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
vg1019872900 2.63E-06 2.63E-06 mr1345_2 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
vg1019872900 NA 9.15E-07 mr1422_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
vg1019872900 NA 1.05E-06 mr1606_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
vg1019872900 NA 5.70E-07 mr1623_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
vg1019872900 NA 1.32E-07 mr1653_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
vg1019872900 6.11E-06 6.11E-06 mr1700_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
vg1019872900 7.99E-06 1.92E-09 mr1905_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