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Detailed information for vg1001242224:

Variant ID: vg1001242224 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1242224
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, G: 0.28, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


ACTGATGTAGAAGCTACAAAGTTAGTACACAATAGTTGCCCTTAATCACCACATAACAAGCCGCCTAGGTGTACAATTGAGCATTATCATGAAATATGAA[C/G]
CAGTACATTAATTCCTATTTTGAATATGATCGTCTTCTCCCGCTGATTCTTTCACCGTATTTCTGATACATATCTAACTATAATTGAACAAGTTTGTCAT

Reverse complement sequence

ATGACAAACTTGTTCAATTATAGTTAGATATGTATCAGAAATACGGTGAAAGAATCAGCGGGAGAAGACGATCATATTCAAAATAGGAATTAATGTACTG[G/C]
TTCATATTTCATGATAATGCTCAATTGTACACCTAGGCGGCTTGTTATGTGGTGATTAAGGGCAACTATTGTGTACTAACTTTGTAGCTTCTACATCAGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.70% 47.20% 0.06% 0.00% NA
All Indica  2759 76.50% 23.50% 0.04% 0.00% NA
All Japonica  1512 6.30% 93.70% 0.00% 0.00% NA
Aus  269 94.10% 5.90% 0.00% 0.00% NA
Indica I  595 97.60% 2.40% 0.00% 0.00% NA
Indica II  465 62.40% 37.60% 0.00% 0.00% NA
Indica III  913 69.00% 31.00% 0.00% 0.00% NA
Indica Intermediate  786 77.60% 22.30% 0.13% 0.00% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 17.10% 82.90% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 93.80% 1.04% 0.00% NA
Intermediate  90 30.00% 68.90% 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
vg1001242224 C -> G LOC_Os10g02980.1 downstream_gene_variant ; 452.0bp to feature; MODIFIER silent_mutation Average:69.969; most accessible tissue: Callus, score: 96.279 N N N N
vg1001242224 C -> G LOC_Os10g02990.1 downstream_gene_variant ; 1254.0bp to feature; MODIFIER silent_mutation Average:69.969; most accessible tissue: Callus, score: 96.279 N N N N
vg1001242224 C -> G LOC_Os10g02980-LOC_Os10g02990 intergenic_region ; MODIFIER silent_mutation Average:69.969; most accessible tissue: Callus, score: 96.279 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001242224 3.63E-09 NA mr1486 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
vg1001242224 2.85E-12 2.91E-11 mr1486 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
vg1001242224 NA 3.65E-25 mr1495 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
vg1001242224 7.86E-08 3.89E-24 mr1548 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
vg1001242224 9.57E-10 1.66E-08 mr1548 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
vg1001242224 NA 5.21E-20 mr1588 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
vg1001242224 1.66E-07 1.48E-07 mr1588 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
vg1001242224 NA 1.54E-06 mr1158_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
vg1001242224 NA 3.90E-27 mr1441_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
vg1001242224 3.45E-10 8.58E-52 mr1486_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
vg1001242224 3.57E-14 2.72E-17 mr1486_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
vg1001242224 NA 1.00E-22 mr1495_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
vg1001242224 1.02E-06 3.77E-25 mr1588_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
vg1001242224 2.82E-09 8.11E-09 mr1588_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
vg1001242224 NA 3.11E-08 mr1645_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
vg1001242224 NA 7.65E-06 mr1648_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
vg1001242224 NA 4.45E-13 mr1904_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
vg1001242224 NA 5.00E-06 mr1971_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