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Detailed information for vg0411807924:

Variant ID: vg0411807924 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 11807924
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.58, T: 0.42, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:


TCGCGGCACGCCATGCCACGTGTTTCTCGGCCTCTGCGAAAGACCGAGGCTCACCGTCGTCGCACGCAAGGTGCAACTGCGCCTCCAGGTCGGGAGGCAC[C/T]
AGTCCCGGCACCGGCTGGTCGCCGAGAAGATCCTCCATCGTACGGTACCGTAGCTGCTCGCCGTCGTGGTACGCGTCGATGCGCTCCCCGTCGTGGGAGA

Reverse complement sequence

TCTCCCACGACGGGGAGCGCATCGACGCGTACCACGACGGCGAGCAGCTACGGTACCGTACGATGGAGGATCTTCTCGGCGACCAGCCGGTGCCGGGACT[G/A]
GTGCCTCCCGACCTGGAGGCGCAGTTGCACCTTGCGTGCGACGACGGTGAGCCTCGGTCTTTCGCAGAGGCCGAGAAACACGTGGCATGGCGTGCCGCGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 30.00% 18.10% 20.46% 31.44% NA
All Indica  2759 42.00% 2.20% 23.49% 32.29% NA
All Japonica  1512 9.80% 50.60% 9.59% 30.03% NA
Aus  269 4.80% 3.00% 53.16% 39.03% NA
Indica I  595 55.10% 1.20% 19.50% 24.20% NA
Indica II  465 24.70% 3.00% 28.60% 43.66% NA
Indica III  913 45.10% 1.90% 26.83% 26.18% NA
Indica Intermediate  786 38.70% 2.90% 19.59% 38.80% NA
Temperate Japonica  767 8.00% 84.60% 0.91% 6.52% NA
Tropical Japonica  504 9.10% 4.60% 17.86% 68.45% NA
Japonica Intermediate  241 17.00% 38.60% 19.92% 24.48% NA
VI/Aromatic  96 81.20% 1.00% 10.42% 7.29% NA
Intermediate  90 23.30% 21.10% 23.33% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0411807924 C -> DEL N N silent_mutation Average:33.393; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg0411807924 C -> T LOC_Os04g20990.1 intron_variant ; MODIFIER silent_mutation Average:33.393; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0411807924 NA 2.62E-08 mr1403 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
vg0411807924 NA 9.33E-07 mr1403 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
vg0411807924 NA 3.47E-06 mr1830 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
vg0411807924 NA 6.01E-08 mr1846 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
vg0411807924 NA 7.49E-11 mr1830_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
vg0411807924 1.59E-06 8.71E-16 mr1846_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
vg0411807924 4.23E-07 1.00E-21 mr1846_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