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Detailed information for vg1007270757:

Variant ID: vg1007270757 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 7270757
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


ACCGCCATCCTTGCCGTACTCGACGATGCGCTGTCCTTCGTCTTCTTTTGCAGTCGCCAGGGAGAAAGAAGTGGGAGATGGAAAAGGGGGAACGAGACGG[C/T]
GTGAGAGAGGAGACAGAAAAAGGGATAAGAGTGGCATGGTTCCAATATTAGAAAATTTCAGTGGCATGTAGCCAATATGATGAATAGTATTGACATTTTT

Reverse complement sequence

AAAAATGTCAATACTATTCATCATATTGGCTACATGCCACTGAAATTTTCTAATATTGGAACCATGCCACTCTTATCCCTTTTTCTGTCTCCTCTCTCAC[G/A]
CCGTCTCGTTCCCCCTTTTCCATCTCCCACTTCTTTCTCCCTGGCGACTGCAAAAGAAGACGAAGGACAGCGCATCGTCGAGTACGGCAAGGATGGCGGT

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 93.10% 4.80% 2.07% 0.00% NA
All Indica  2759 99.80% 0.10% 0.11% 0.00% NA
All Japonica  1512 79.20% 14.60% 6.28% 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 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.00% 0.38% 0.00% NA
Temperate Japonica  767 61.90% 27.80% 10.30% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 90.90% 2.90% 6.22% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1007270757 C -> T LOC_Os10g13450.1 upstream_gene_variant ; 93.0bp to feature; MODIFIER silent_mutation Average:68.19; most accessible tissue: Zhenshan97 young leaf, score: 89.772 N N N N
vg1007270757 C -> T LOC_Os10g13440.1 downstream_gene_variant ; 941.0bp to feature; MODIFIER silent_mutation Average:68.19; most accessible tissue: Zhenshan97 young leaf, score: 89.772 N N N N
vg1007270757 C -> T LOC_Os10g13460.1 downstream_gene_variant ; 629.0bp to feature; MODIFIER silent_mutation Average:68.19; most accessible tissue: Zhenshan97 young leaf, score: 89.772 N N N N
vg1007270757 C -> T LOC_Os10g13450-LOC_Os10g13460 intergenic_region ; MODIFIER silent_mutation Average:68.19; most accessible tissue: Zhenshan97 young leaf, score: 89.772 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1007270757 7.19E-07 NA mr1768 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
vg1007270757 NA 3.08E-06 mr1768 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
vg1007270757 1.77E-11 2.78E-28 mr1768_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
vg1007270757 7.09E-06 8.66E-10 mr1768_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