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Detailed information for vg1004284387:

Variant ID: vg1004284387 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4284387
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CATATCTCAGAAATAGGTATACCAATGGGAAGATAACAAGACAAGGTGACAGAAGAAACATGGCAATACCCATAAATACAAGCCGTTTCTTCAATAAAGA[C/T]
GGACTTGTCAGAATGTCTTTTCTAACACAAAATTTCCTGCAGCAGAACAGGATGTGAGTTTTGAACAGAGAAGAATAGTACATAGTCCAAAAAGATGGAA

Reverse complement sequence

TTCCATCTTTTTGGACTATGTACTATTCTTCTCTGTTCAAAACTCACATCCTGTTCTGCTGCAGGAAATTTTGTGTTAGAAAAGACATTCTGACAAGTCC[G/A]
TCTTTATTGAAGAAACGGCTTGTATTTATGGGTATTGCCATGTTTCTTCTGTCACCTTGTCTTGTTATCTTCCCATTGGTATACCTATTTCTGAGATATG

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 56.10% 43.70% 0.21% 0.00% NA
All Indica  2759 42.80% 56.90% 0.29% 0.00% NA
All Japonica  1512 74.70% 25.20% 0.07% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 60.00% 39.50% 0.50% 0.00% NA
Indica II  465 37.40% 62.20% 0.43% 0.00% NA
Indica III  913 31.20% 68.70% 0.11% 0.00% NA
Indica Intermediate  786 46.40% 53.30% 0.25% 0.00% NA
Temperate Japonica  767 93.90% 6.00% 0.13% 0.00% NA
Tropical Japonica  504 54.80% 45.20% 0.00% 0.00% NA
Japonica Intermediate  241 55.60% 44.40% 0.00% 0.00% NA
VI/Aromatic  96 34.40% 65.60% 0.00% 0.00% NA
Intermediate  90 47.80% 51.10% 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
vg1004284387 C -> T LOC_Os10g07994.1 synonymous_variant ; p.Pro311Pro; LOW synonymous_codon Average:42.132; most accessible tissue: Zhenshan97 young leaf, score: 66.83 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004284387 9.99E-06 2.28E-10 mr1603 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
vg1004284387 NA 9.49E-07 mr1603 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
vg1004284387 NA 8.07E-08 mr1495_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
vg1004284387 NA 3.93E-08 mr1603_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
vg1004284387 NA 7.16E-06 mr1603_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