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Detailed information for vg1216454490:

Variant ID: vg1216454490 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16454490
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.58, C: 0.42, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:


GATGATCTGAGCGGTCAAACTTAATTGCTATCTCTGACCACCGAAGATATTGGGGCGTGTTAGGCTAAACTGCATTGATCTCCAGTTCTGTTAACTTCTG[C/T]
TTTCTCTTAGATTCATAAGTCAGGGGTCCGCCGAAGATGTGATTGAGTTCTTTGCGATGATCTTGAAAACCAGTCGGGGCATCGTCTTCATCATCTTTCT

Reverse complement sequence

AGAAAGATGATGAAGACGATGCCCCGACTGGTTTTCAAGATCATCGCAAAGAACTCAATCACATCTTCGGCGGACCCCTGACTTATGAATCTAAGAGAAA[G/A]
CAGAAGTTAACAGAACTGGAGATCAATGCAGTTTAGCCTAACACGCCCCAATATCTTCGGTGGTCAGAGATAGCAATTAAGTTTGACCGCTCAGATCATC

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 18.60% 4.40% 21.27% 55.69% NA
All Indica  2759 4.30% 5.10% 22.58% 68.00% NA
All Japonica  1512 48.60% 2.80% 21.56% 27.05% NA
Aus  269 1.50% 3.70% 5.58% 89.22% NA
Indica I  595 4.50% 1.00% 14.45% 80.00% NA
Indica II  465 5.80% 9.90% 55.70% 28.60% NA
Indica III  913 1.90% 3.80% 9.75% 84.56% NA
Indica Intermediate  786 6.00% 7.00% 24.05% 62.98% NA
Temperate Japonica  767 79.00% 1.20% 3.26% 16.56% NA
Tropical Japonica  504 5.00% 5.80% 50.20% 39.09% NA
Japonica Intermediate  241 43.20% 1.70% 19.92% 35.27% NA
VI/Aromatic  96 1.00% 2.10% 23.96% 72.92% NA
Intermediate  90 25.60% 13.30% 20.00% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216454490 C -> DEL LOC_Os12g27910.1 N frameshift_variant Average:15.257; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1216454490 C -> T LOC_Os12g27910.1 synonymous_variant ; p.Lys651Lys; LOW synonymous_codon Average:15.257; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216454490 2.83E-06 NA mr1142 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
vg1216454490 7.24E-06 NA mr1489 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
vg1216454490 NA 3.53E-07 mr1072_2 Jap_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
vg1216454490 NA 2.92E-06 mr1075_2 Jap_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
vg1216454490 NA 1.05E-11 mr1089_2 Jap_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
vg1216454490 NA 8.41E-08 mr1129_2 Jap_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
vg1216454490 NA 7.04E-09 mr1251_2 Jap_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
vg1216454490 NA 1.03E-10 mr1257_2 Jap_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
vg1216454490 NA 3.00E-06 mr1423_2 Jap_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
vg1216454490 NA 6.30E-09 mr1435_2 Jap_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
vg1216454490 9.65E-06 9.65E-06 mr1541_2 Jap_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
vg1216454490 NA 8.96E-07 mr1629_2 Jap_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