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Search for Variation information by Variation ID:

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

Detailed information for vg0728021019:

Variant ID: vg0728021019 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 28021019
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: 108. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCCGTCATCACCGGCGGCGCCAGCGGCATCGGCAAGGCGACGGCCACGGAGTTCATCAAGAACGGCGCCAAGGTCATCATCGCCGACATCCAGGACGA[C/T]
CTCGGCCACTCGGTGGCGGCGGAGCTCGGCCCGGACGCCGCGTACACGCGCTGCGACGTCGCCGACGAGGCGCAGGTCGCCGCGGCCGTGGGCCTCGCCG

Reverse complement sequence

CGGCGAGGCCCACGGCCGCGGCGACCTGCGCCTCGTCGGCGACGTCGCAGCGCGTGTACGCGGCGTCCGGGCCGAGCTCCGCCGCCACCGAGTGGCCGAG[G/A]
TCGTCCTGGATGTCGGCGATGATGACCTTGGCGCCGTTCTTGATGAACTCCGTGGCCGTCGCCTTGCCGATGCCGCTGGCGCCGCCGGTGATGACGGCCA

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 69.90% 13.40% 9.31% 7.38% NA
All Indica  2759 49.30% 22.50% 15.66% 12.47% NA
All Japonica  1512 99.40% 0.30% 0.13% 0.13% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 58.00% 12.10% 22.02% 7.90% NA
Indica II  465 30.30% 42.20% 18.49% 9.03% NA
Indica III  913 51.70% 20.90% 9.20% 18.18% NA
Indica Intermediate  786 51.30% 20.70% 16.67% 11.32% NA
Temperate Japonica  767 99.10% 0.70% 0.13% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.41% 0.41% NA
VI/Aromatic  96 96.90% 1.00% 2.08% 0.00% NA
Intermediate  90 84.40% 7.80% 4.44% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0728021019 C -> DEL LOC_Os07g46870.1 N frameshift_variant Average:72.373; most accessible tissue: Zhenshan97 root, score: 86.472 N N N N
vg0728021019 C -> T LOC_Os07g46870.1 synonymous_variant ; p.Asp77Asp; LOW synonymous_codon Average:72.373; most accessible tissue: Zhenshan97 root, score: 86.472 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0728021019 NA 3.76E-07 mr1032 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
vg0728021019 NA 4.28E-08 mr1165 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
vg0728021019 1.30E-06 1.30E-06 mr1460 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
vg0728021019 NA 8.57E-08 mr1478 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
vg0728021019 NA 6.03E-06 mr1502 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
vg0728021019 NA 3.10E-11 mr1720 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
vg0728021019 NA 1.22E-06 mr1720 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
vg0728021019 NA 1.10E-06 mr1165_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
vg0728021019 2.64E-06 NA mr1457_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
vg0728021019 1.76E-07 4.84E-09 mr1457_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
vg0728021019 NA 5.54E-07 mr1478_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