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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0907672928:

Variant ID: vg0907672928 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7672928
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTGGCCCTCATCGACTCGAGCTTTTCGTCGAATTCAGATGTCAGCTCAGCTCTTATCGACGCCCGGATCTTGGCTTCAAGGCGTGCATCTTTCTTCGC[C/T]
TTTTTGGAAGTCCGCTTCTTGTACTGCCAAGCGTAGTCTGGAAATCCATACTTCTAGGGAACAGAAGACCCAACGCCCCGTGTCTGTCCATAGTGTTCCT

Reverse complement sequence

AGGAACACTATGGACAGACACGGGGCGTTGGGTCTTCTGTTCCCTAGAAGTATGGATTTCCAGACTACGCTTGGCAGTACAAGAAGCGGACTTCCAAAAA[G/A]
GCGAAGAAAGATGCACGCCTTGAAGCCAAGATCCGGGCGTCGATAAGAGCTGAGCTGACATCTGAATTCGACGAAAAGCTCGAGTCGATGAGGGCCAAGA

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 26.90% 14.60% 9.56% 48.88% NA
All Indica  2759 11.00% 5.60% 15.04% 68.32% NA
All Japonica  1512 57.30% 29.20% 1.79% 11.64% NA
Aus  269 14.10% 1.90% 2.23% 81.78% NA
Indica I  595 7.10% 5.00% 14.62% 73.28% NA
Indica II  465 6.70% 2.40% 5.16% 85.81% NA
Indica III  913 15.30% 6.90% 22.78% 54.98% NA
Indica Intermediate  786 11.60% 6.50% 12.21% 69.72% NA
Temperate Japonica  767 66.90% 9.50% 3.00% 20.60% NA
Tropical Japonica  504 34.70% 63.50% 0.40% 1.39% NA
Japonica Intermediate  241 74.30% 20.30% 0.83% 4.56% NA
VI/Aromatic  96 32.30% 62.50% 1.04% 4.17% NA
Intermediate  90 36.70% 32.20% 3.33% 27.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0907672928 C -> DEL LOC_Os09g13300.1 N frameshift_variant Average:9.49; most accessible tissue: Callus, score: 25.426 N N N N
vg0907672928 C -> T LOC_Os09g13300.1 synonymous_variant ; p.Lys65Lys; LOW synonymous_codon Average:9.49; most accessible tissue: Callus, score: 25.426 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907672928 NA 6.39E-08 mr1002 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
vg0907672928 NA 9.90E-11 mr1070 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
vg0907672928 NA 6.92E-11 mr1128 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
vg0907672928 NA 7.61E-07 mr1438 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
vg0907672928 NA 4.76E-07 mr1642 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
vg0907672928 6.21E-06 6.27E-06 mr1994 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
vg0907672928 NA 1.88E-09 mr1002_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
vg0907672928 NA 2.89E-09 mr1438_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
vg0907672928 4.68E-06 4.68E-06 mr1438_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
vg0907672928 NA 2.36E-06 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