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

Detailed information for vg0511404761:

Variant ID: vg0511404761 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 11404761
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGTACGCATGGCAGCACAAGAAGCAGACCTCCAACAAGGCGCAAAATTTATCGCCAAGATCCGGGAGTCGATCAGAGCCGAGTGACCTCTGAATTCGA[C/T]
GAGAAGCTTTGAGAAGAGCAACAGAACCCGGAGGCTGCCGCTGCTGCTGCGCAAGAAGAGTTAGCAGGTCCCACCCAAAGGCGCAGCAGTTGCGCATCAA

Reverse complement sequence

TTGATGCGCAACTGCTGCGCCTTTGGGTGGGACCTGCTAACTCTTCTTGCGCAGCAGCAGCGGCAGCCTCCGGGTTCTGTTGCTCTTCTCAAAGCTTCTC[G/A]
TCGAATTCAGAGGTCACTCGGCTCTGATCGACTCCCGGATCTTGGCGATAAATTTTGCGCCTTGTTGGAGGTCTGCTTCTTGTGCTGCCATGCGTACTCT

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 87.70% 12.10% 0.21% 0.00% NA
All Indica  2759 89.30% 10.60% 0.04% 0.00% NA
All Japonica  1512 96.00% 3.40% 0.60% 0.00% NA
Aus  269 20.40% 79.60% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.50% 1.30% 0.22% 0.00% NA
Indica III  913 79.00% 21.00% 0.00% 0.00% NA
Indica Intermediate  786 88.30% 11.70% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 89.90% 8.70% 1.39% 0.00% NA
Japonica Intermediate  241 95.90% 3.30% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 0.00% 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
vg0511404761 C -> T LOC_Os05g19580.1 intron_variant ; MODIFIER silent_mutation Average:49.981; most accessible tissue: Zhenshan97 young leaf, score: 73.923 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0511404761 NA 2.46E-09 mr1317 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
vg0511404761 NA 5.98E-07 mr1343 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
vg0511404761 NA 3.29E-07 mr1530 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
vg0511404761 NA 1.27E-10 mr1317_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
vg0511404761 NA 6.13E-06 mr1608_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
vg0511404761 NA 6.88E-12 mr1610_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
vg0511404761 NA 1.51E-08 mr1642_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
vg0511404761 NA 1.65E-11 mr1818_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
vg0511404761 5.23E-08 NA mr1850_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
vg0511404761 NA 5.16E-11 mr1897_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
vg0511404761 NA 2.79E-12 mr1914_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
vg0511404761 NA 3.73E-17 mr1927_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