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Detailed information for vg1014019485:

Variant ID: vg1014019485 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 14019485
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGGTGCAGGTTTTTCCCTAGAATAAATTAATGGTGGGATTTTATTAATTAATCGGCACCGAATTTTTAATTAACCGACATCTATAATAAATTAATGGTG[C/T]
GAGTTTTTTTAAAACAACTGGCATCTATAGCATGGGTGCCGGTTTTTCCCTAGAACCGCACCTATTTCTTCACAAAGGTGCCGGTTTTAGTTGATGGTGC

Reverse complement sequence

GCACCATCAACTAAAACCGGCACCTTTGTGAAGAAATAGGTGCGGTTCTAGGGAAAAACCGGCACCCATGCTATAGATGCCAGTTGTTTTAAAAAAACTC[G/A]
CACCATTAATTTATTATAGATGTCGGTTAATTAAAAATTCGGTGCCGATTAATTAATAAAATCCCACCATTAATTTATTCTAGGGAAAAACCTGCACCCA

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 81.70% 3.80% 10.88% 3.55% NA
All Indica  2759 69.00% 6.50% 18.45% 6.05% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 53.30% 5.20% 35.46% 6.05% NA
Indica II  465 77.00% 5.40% 12.04% 5.59% NA
Indica III  913 73.80% 8.80% 11.94% 5.48% NA
Indica Intermediate  786 70.50% 5.60% 16.92% 7.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 1.10% 5.56% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1014019485 C -> T LOC_Os10g26780-LOC_Os10g26800 intergenic_region ; MODIFIER silent_mutation Average:44.248; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg1014019485 C -> DEL N N silent_mutation Average:44.248; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1014019485 NA 7.48E-06 mr1446 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
vg1014019485 2.00E-06 NA mr1577 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
vg1014019485 2.84E-06 6.12E-08 mr1577 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
vg1014019485 NA 3.50E-07 mr1734 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
vg1014019485 NA 9.59E-07 mr1780 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
vg1014019485 6.67E-07 8.13E-09 mr1792 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
vg1014019485 5.14E-06 6.28E-08 mr1792 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