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Detailed information for vg1005803839:

Variant ID: vg1005803839 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5803839
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.23, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


CTAAACTCGAAACCCTAACTCAAAACTTAACTCAATTGCTCTCTAAAGCGATACCGGGAAGCCTCACGCTCCCCCCTCTATTTATACATGAGGTAGGCAG[C/T]
CTAAAGCCCCGAACCAAACTCATACTAGGAGTCCTAAACACCTTAGGAAACCCACTAGTACAAGAAAGAAACTTTACATAACCAAACGTACCAAATTTGG

Reverse complement sequence

CCAAATTTGGTACGTTTGGTTATGTAAAGTTTCTTTCTTGTACTAGTGGGTTTCCTAAGGTGTTTAGGACTCCTAGTATGAGTTTGGTTCGGGGCTTTAG[G/A]
CTGCCTACCTCATGTATAAATAGAGGGGGGAGCGTGAGGCTTCCCGGTATCGCTTTAGAGAGCAATTGAGTTAAGTTTTGAGTTAGGGTTTCGAGTTTAG

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 77.00% 21.20% 1.84% 0.00% NA
All Indica  2759 72.40% 26.30% 1.34% 0.00% NA
All Japonica  1512 98.70% 1.20% 0.13% 0.00% NA
Aus  269 4.50% 82.20% 13.38% 0.00% NA
Indica I  595 90.30% 8.90% 0.84% 0.00% NA
Indica II  465 71.40% 26.70% 1.94% 0.00% NA
Indica III  913 68.00% 31.10% 0.88% 0.00% NA
Indica Intermediate  786 64.50% 33.60% 1.91% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.40% 0.20% 0.00% NA
Japonica Intermediate  241 95.00% 4.60% 0.41% 0.00% NA
VI/Aromatic  96 65.60% 22.90% 11.46% 0.00% NA
Intermediate  90 81.10% 17.80% 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
vg1005803839 C -> T LOC_Os10g10520.1 upstream_gene_variant ; 838.0bp to feature; MODIFIER silent_mutation Average:35.67; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg1005803839 C -> T LOC_Os10g10520-LOC_Os10g10530 intergenic_region ; MODIFIER silent_mutation Average:35.67; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005803839 NA 3.99E-10 mr1027_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
vg1005803839 NA 4.64E-06 mr1057_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
vg1005803839 NA 4.46E-06 mr1555_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
vg1005803839 NA 2.50E-09 mr1580_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
vg1005803839 NA 5.83E-07 mr1691_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
vg1005803839 NA 4.07E-06 mr1693_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
vg1005803839 NA 1.86E-10 mr1709_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
vg1005803839 NA 9.24E-09 mr1741_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
vg1005803839 NA 3.80E-09 mr1743_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
vg1005803839 NA 9.08E-06 mr1743_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
vg1005803839 NA 2.26E-06 mr1785_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
vg1005803839 NA 7.20E-10 mr1825_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