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Detailed information for vg1005270327:

Variant ID: vg1005270327 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5270327
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.77, G: 0.23, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTCTTTGCTCCCTATTAGTAACAGCAACCGGTACCAACCGGGACAAAAAGATTGATTATTTCAACCGAGACTAGTCCTGGATTGCTACTCCCGGTTG[A/G]
AAAACCGAGACTAAAAGGGGTTAACAACCGGGAGTAAAAATAGTTTCTCCACCAGTGGATGGACCTGTATATCCCCCGACGTGAAGGCCACGGAATGGAG

Reverse complement sequence

CTCCATTCCGTGGCCTTCACGTCGGGGGATATACAGGTCCATCCACTGGTGGAGAAACTATTTTTACTCCCGGTTGTTAACCCCTTTTAGTCTCGGTTTT[T/C]
CAACCGGGAGTAGCAATCCAGGACTAGTCTCGGTTGAAATAATCAATCTTTTTGTCCCGGTTGGTACCGGTTGCTGTTACTAATAGGGAGCAAAGAAAAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.20% 41.30% 0.40% 4.08% NA
All Indica  2759 41.40% 58.00% 0.25% 0.36% NA
All Japonica  1512 86.20% 3.40% 0.40% 9.99% NA
Aus  269 3.70% 94.40% 1.49% 0.37% NA
Indica I  595 21.30% 78.70% 0.00% 0.00% NA
Indica II  465 51.20% 48.40% 0.43% 0.00% NA
Indica III  913 53.20% 45.90% 0.22% 0.66% NA
Indica Intermediate  786 37.20% 62.00% 0.38% 0.51% NA
Temperate Japonica  767 78.70% 3.50% 0.65% 17.08% NA
Tropical Japonica  504 97.00% 2.00% 0.20% 0.79% NA
Japonica Intermediate  241 87.60% 5.80% 0.00% 6.64% NA
VI/Aromatic  96 50.00% 24.00% 1.04% 25.00% NA
Intermediate  90 64.40% 26.70% 1.11% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005270327 A -> G LOC_Os10g09740.1 intron_variant ; MODIFIER silent_mutation Average:65.079; most accessible tissue: Zhenshan97 young leaf, score: 87.443 N N N N
vg1005270327 A -> DEL N N silent_mutation Average:65.079; most accessible tissue: Zhenshan97 young leaf, score: 87.443 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005270327 NA 2.08E-06 mr1210 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
vg1005270327 3.81E-07 1.20E-09 mr1300 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
vg1005270327 NA 6.82E-07 mr1305 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
vg1005270327 NA 2.00E-07 mr1310 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
vg1005270327 NA 1.29E-06 mr1420 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
vg1005270327 NA 3.63E-09 mr1585 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
vg1005270327 NA 6.58E-09 mr1585 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
vg1005270327 NA 4.42E-06 mr1586 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
vg1005270327 NA 2.55E-06 mr1665 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
vg1005270327 NA 1.08E-07 mr1926 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
vg1005270327 9.64E-06 NA mr1305_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
vg1005270327 NA 1.42E-07 mr1305_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
vg1005270327 9.25E-06 3.70E-08 mr1585_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
vg1005270327 NA 1.77E-09 mr1585_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
vg1005270327 NA 1.14E-08 mr1765_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
vg1005270327 NA 4.92E-06 mr1765_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
vg1005270327 NA 6.75E-06 mr1942_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