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Detailed information for vg1126338061:

Variant ID: vg1126338061 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26338061
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, C: 0.08, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


CACGAAATAAATTGGAGTAATGAAAAGTGATATATGTCTGTATAGATCCATGACATATTTAATTAATCAACGAATGGTTTATATAAATTGGAGCGCAAAA[C/A]
GAGAGCAATCGATGAAGTACCCCAGGCTGATCAAGAAAAGAAACTAAACAATCAACAGAAAAATGTAGAGATGGTCATGATCATCACATTCATATATATA

Reverse complement sequence

TATATATATGAATGTGATGATCATGACCATCTCTACATTTTTCTGTTGATTGTTTAGTTTCTTTTCTTGATCAGCCTGGGGTACTTCATCGATTGCTCTC[G/T]
TTTTGCGCTCCAATTTATATAAACCATTCGTTGATTAATTAAATATGTCATGGATCTATACAGACATATATCACTTTTCATTACTCCAATTTATTTCGTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.00% 16.40% 0.57% 1.08% NA
All Indica  2759 86.20% 12.80% 0.33% 0.76% NA
All Japonica  1512 77.30% 21.60% 1.06% 0.00% NA
Aus  269 60.20% 28.60% 0.00% 11.15% NA
Indica I  595 74.10% 24.20% 0.17% 1.51% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 95.10% 4.50% 0.00% 0.44% NA
Indica Intermediate  786 78.50% 19.50% 1.02% 1.02% NA
Temperate Japonica  767 62.30% 35.70% 1.96% 0.00% NA
Tropical Japonica  504 97.40% 2.60% 0.00% 0.00% NA
Japonica Intermediate  241 83.00% 16.60% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 78.90% 20.00% 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
vg1126338061 C -> A LOC_Os11g43650-LOC_Os11g43660 intergenic_region ; MODIFIER silent_mutation Average:43.953; most accessible tissue: Zhenshan97 young leaf, score: 59.612 N N N N
vg1126338061 C -> DEL N N silent_mutation Average:43.953; most accessible tissue: Zhenshan97 young leaf, score: 59.612 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126338061 NA 7.35E-07 mr1130 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
vg1126338061 2.02E-08 7.41E-10 mr1191 Ind_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
vg1126338061 NA 1.38E-06 mr1542 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
vg1126338061 1.41E-07 2.03E-08 mr1644 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
vg1126338061 NA 5.01E-07 mr1191_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
vg1126338061 NA 6.57E-06 mr1206_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
vg1126338061 NA 2.20E-08 mr1542_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