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Detailed information for vg0405360103:

Variant ID: vg0405360103 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5360103
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


TAGAATATCGCAAACCACCATGGCATTCATCACATAAAATCTAAATCAACTCCATGTTTCTACTAATCTATGTATTATTATATAATAAAAGTCCATTAAA[C/T]
TTCCTATAAACGCTCCTAAGCCGCCACATGGCACTCCTACAAAAGCTATAAAGCCGTTATGTGGCACTCAAATAAATTATAGAAATTATGTAAATTATGT

Reverse complement sequence

ACATAATTTACATAATTTCTATAATTTATTTGAGTGCCACATAACGGCTTTATAGCTTTTGTAGGAGTGCCATGTGGCGGCTTAGGAGCGTTTATAGGAA[G/A]
TTTAATGGACTTTTATTATATAATAATACATAGATTAGTAGAAACATGGAGTTGATTTAGATTTTATGTGATGAATGCCATGGTGGTTTGCGATATTCTA

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 59.60% 40.00% 0.30% 0.06% NA
All Indica  2759 81.80% 17.70% 0.43% 0.07% NA
All Japonica  1512 10.40% 89.60% 0.07% 0.00% NA
Aus  269 98.50% 0.70% 0.37% 0.37% NA
Indica I  595 93.10% 5.50% 1.34% 0.00% NA
Indica II  465 87.50% 12.30% 0.22% 0.00% NA
Indica III  913 69.40% 30.20% 0.11% 0.22% NA
Indica Intermediate  786 84.40% 15.40% 0.25% 0.00% NA
Temperate Japonica  767 8.20% 91.80% 0.00% 0.00% NA
Tropical Japonica  504 13.90% 86.10% 0.00% 0.00% NA
Japonica Intermediate  241 10.00% 89.60% 0.41% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 58.90% 41.10% 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
vg0405360103 C -> DEL N N silent_mutation Average:39.813; most accessible tissue: Minghui63 flag leaf, score: 53.617 N N N N
vg0405360103 C -> T LOC_Os04g09950.1 downstream_gene_variant ; 2312.0bp to feature; MODIFIER silent_mutation Average:39.813; most accessible tissue: Minghui63 flag leaf, score: 53.617 N N N N
vg0405360103 C -> T LOC_Os04g09960.1 downstream_gene_variant ; 364.0bp to feature; MODIFIER silent_mutation Average:39.813; most accessible tissue: Minghui63 flag leaf, score: 53.617 N N N N
vg0405360103 C -> T LOC_Os04g09960-LOC_Os04g09980 intergenic_region ; MODIFIER silent_mutation Average:39.813; most accessible tissue: Minghui63 flag leaf, score: 53.617 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405360103 NA 7.24E-11 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0405360103 NA 3.21E-10 mr1023 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
vg0405360103 9.95E-07 1.19E-20 mr1035 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
vg0405360103 NA 3.99E-06 mr1035 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
vg0405360103 NA 2.06E-47 mr1136 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
vg0405360103 NA 3.81E-06 mr1203 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
vg0405360103 NA 7.36E-07 mr1395 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
vg0405360103 4.40E-06 NA mr1419 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
vg0405360103 NA 8.59E-07 mr1489 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
vg0405360103 NA 9.33E-06 mr1618 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
vg0405360103 3.39E-06 3.26E-17 mr1626 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
vg0405360103 NA 8.94E-06 mr1626 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
vg0405360103 1.72E-06 1.10E-32 mr1631 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
vg0405360103 7.96E-06 1.30E-06 mr1631 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
vg0405360103 NA 2.59E-09 mr1637 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
vg0405360103 NA 3.49E-13 mr1740 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
vg0405360103 NA 7.29E-10 mr1905 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
vg0405360103 NA 1.46E-16 mr1035_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
vg0405360103 NA 9.80E-18 mr1062_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
vg0405360103 NA 1.96E-52 mr1136_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
vg0405360103 NA 1.36E-18 mr1167_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
vg0405360103 NA 1.18E-29 mr1631_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