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Detailed information for vg0715489455:

Variant ID: vg0715489455 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15489455
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


CCCAAGCGACCAACCGTCGACTGGAAACCAGTCGGCTGAAGCGGAAACCGCTGCTAGCCAGGAGCCCCCGACTGGAAACCAGTCGGAAGCAGGACCAAGC[C/T]
AGGAAATCCCTGGGATTGAAACTCAGGCAAATGCTTTCCAAGAACCAAACGCTGATAACGATCCGACACCCGGGTCATCAGATAAAGGGCAAGGATCACC

Reverse complement sequence

GGTGATCCTTGCCCTTTATCTGATGACCCGGGTGTCGGATCGTTATCAGCGTTTGGTTCTTGGAAAGCATTTGCCTGAGTTTCAATCCCAGGGATTTCCT[G/A]
GCTTGGTCCTGCTTCCGACTGGTTTCCAGTCGGGGGCTCCTGGCTAGCAGCGGTTTCCGCTTCAGCCGACTGGTTTCCAGTCGACGGTTGGTCGCTTGGG

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 60.90% 16.60% 2.37% 20.06% NA
All Indica  2759 71.30% 24.90% 1.45% 2.39% NA
All Japonica  1512 46.60% 2.20% 0.79% 50.40% NA
Aus  269 49.80% 20.10% 17.47% 12.64% NA
Indica I  595 69.60% 27.40% 1.01% 2.02% NA
Indica II  465 89.00% 4.30% 2.58% 4.09% NA
Indica III  913 59.10% 39.80% 0.77% 0.33% NA
Indica Intermediate  786 76.10% 17.90% 1.91% 4.07% NA
Temperate Japonica  767 76.30% 0.80% 0.39% 22.56% NA
Tropical Japonica  504 8.10% 5.00% 1.39% 85.52% NA
Japonica Intermediate  241 32.80% 0.80% 0.83% 65.56% NA
VI/Aromatic  96 19.80% 1.00% 4.17% 75.00% NA
Intermediate  90 62.20% 12.20% 10.00% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0715489455 C -> DEL LOC_Os07g26800.1 N frameshift_variant Average:54.931; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 N N N N
vg0715489455 C -> T LOC_Os07g26800.1 stop_gained ; p.Gln391*; HIGH stop_gained Average:54.931; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715489455 2.99E-07 4.81E-09 mr1519 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
vg0715489455 NA 6.14E-07 mr1045_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
vg0715489455 NA 6.65E-07 mr1105_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
vg0715489455 NA 9.86E-07 mr1232_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
vg0715489455 4.65E-07 NA mr1519_2 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
vg0715489455 9.72E-07 7.17E-14 mr1519_2 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
vg0715489455 NA 1.38E-06 mr1901_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
vg0715489455 3.52E-06 3.51E-06 mr1953_2 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