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Detailed information for vg1016117610:

Variant ID: vg1016117610 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 16117610
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.56, C: 0.44, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


TGCATTATCAAATTAGTTTTATTAAATTAATAATTAAATATATTTTTATAATAAATTTATCTTGGATAAAAAATATTACTATTTTTTCTATAAACTTAGT[T/C]
AAACTTAAAGTAGTTTGACTTTGATCAAAGTCAAAACATTTTATAATCTGAAACGAAGGGAGTAGATAATACCCCTTTAGCTATGTCCAAAATTCTCCGG

Reverse complement sequence

CCGGAGAATTTTGGACATAGCTAAAGGGGTATTATCTACTCCCTTCGTTTCAGATTATAAAATGTTTTGACTTTGATCAAAGTCAAACTACTTTAAGTTT[A/G]
ACTAAGTTTATAGAAAAAATAGTAATATTTTTTATCCAAGATAAATTTATTATAAAAATATATTTAATTATTAATTTAATAAAACTAATTTGATAATGCA

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 75.70% 21.10% 1.84% 1.40% NA
All Indica  2759 93.40% 1.30% 3.04% 2.25% NA
All Japonica  1512 38.40% 61.30% 0.07% 0.26% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 89.70% 0.80% 7.06% 2.35% NA
Indica II  465 92.50% 1.90% 2.58% 3.01% NA
Indica III  913 97.30% 0.30% 0.66% 1.75% NA
Indica Intermediate  786 92.10% 2.50% 3.05% 2.29% NA
Temperate Japonica  767 3.80% 96.20% 0.00% 0.00% NA
Tropical Japonica  504 92.50% 6.90% 0.20% 0.40% NA
Japonica Intermediate  241 35.30% 63.90% 0.00% 0.83% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 77.80% 20.00% 2.22% 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
vg1016117610 T -> C LOC_Os10g30900.1 upstream_gene_variant ; 2458.0bp to feature; MODIFIER silent_mutation Average:40.364; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg1016117610 T -> C LOC_Os10g30910.1 upstream_gene_variant ; 3621.0bp to feature; MODIFIER silent_mutation Average:40.364; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg1016117610 T -> C LOC_Os10g30910.2 upstream_gene_variant ; 4452.0bp to feature; MODIFIER silent_mutation Average:40.364; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg1016117610 T -> C LOC_Os10g30900-LOC_Os10g30910 intergenic_region ; MODIFIER silent_mutation Average:40.364; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg1016117610 T -> DEL N N silent_mutation Average:40.364; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1016117610 NA 1.49E-06 mr1328 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
vg1016117610 4.74E-06 5.24E-09 mr1530 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
vg1016117610 NA 2.11E-10 mr1539 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
vg1016117610 NA 3.25E-15 mr1540 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
vg1016117610 NA 3.15E-21 mr1679 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
vg1016117610 NA 9.90E-10 mr1691 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
vg1016117610 NA 8.61E-10 mr1693 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
vg1016117610 NA 2.12E-06 mr1704 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
vg1016117610 NA 1.50E-18 mr1732 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
vg1016117610 NA 7.86E-06 mr1736 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
vg1016117610 NA 7.18E-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
vg1016117610 NA 1.42E-10 mr1790 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
vg1016117610 NA 2.66E-06 mr1815 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
vg1016117610 NA 4.29E-33 mr1980 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
vg1016117610 NA 2.42E-09 mr1980 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
vg1016117610 NA 6.20E-14 mr1982 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
vg1016117610 NA 1.72E-07 mr1125_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
vg1016117610 NA 3.62E-08 mr1156_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
vg1016117610 NA 4.54E-08 mr1189_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
vg1016117610 NA 9.22E-08 mr1446_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
vg1016117610 NA 6.41E-07 mr1446_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
vg1016117610 NA 7.36E-07 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
vg1016117610 NA 3.15E-42 mr1533_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
vg1016117610 NA 4.20E-12 mr1533_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
vg1016117610 NA 1.28E-19 mr1539_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
vg1016117610 4.20E-06 7.86E-18 mr1539_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
vg1016117610 NA 1.88E-19 mr1540_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
vg1016117610 NA 4.67E-19 mr1540_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
vg1016117610 NA 8.34E-19 mr1732_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
vg1016117610 NA 1.35E-17 mr1732_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
vg1016117610 NA 1.29E-08 mr1879_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
vg1016117610 NA 2.78E-06 mr1966_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
vg1016117610 NA 3.75E-21 mr1980_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
vg1016117610 NA 6.36E-07 mr1980_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