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Detailed information for vg1002269285:

Variant ID: vg1002269285 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2269285
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.53, C: 0.47, others allele: 0.00, population size: 57. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGAAACTGAAAGCAAATTGTACTTTAAATCCTCAACCAAAGCTACATTCTTCAATTCAAATTTTTCATTTACCTTAACCGAACCTGTAGCGAGAATGG[A/C]
ACTTGTAGAAGCATCACGAAAGATAATCGATTCAGTCTTGGATGCCTTTTTGAGGGAGGAGAACCAATTTTTATCACCGGTCATGTGCCGCGAACAACCG

Reverse complement sequence

CGGTTGTTCGCGGCACATGACCGGTGATAAAAATTGGTTCTCCTCCCTCAAAAAGGCATCCAAGACTGAATCGATTATCTTTCGTGATGCTTCTACAAGT[T/G]
CCATTCTCGCTACAGGTTCGGTTAAGGTAAATGAAAAATTTGAATTGAAGAATGTAGCTTTGGTTGAGGATTTAAAGTACAATTTGCTTTCAGTTTCACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 24.60% 15.30% 2.90% 57.19% NA
All Indica  2759 4.70% 12.00% 3.23% 80.07% NA
All Japonica  1512 60.00% 24.70% 0.46% 14.81% NA
Aus  269 13.00% 1.10% 2.97% 82.90% NA
Indica I  595 3.70% 26.40% 5.71% 64.20% NA
Indica II  465 2.20% 2.20% 2.58% 93.12% NA
Indica III  913 4.50% 11.80% 3.18% 80.50% NA
Indica Intermediate  786 7.40% 7.00% 1.78% 83.84% NA
Temperate Japonica  767 51.20% 40.00% 0.13% 8.60% NA
Tropical Japonica  504 75.80% 3.20% 0.40% 20.63% NA
Japonica Intermediate  241 54.80% 21.20% 1.66% 22.41% NA
VI/Aromatic  96 64.60% 1.00% 28.12% 6.25% NA
Intermediate  90 30.00% 17.80% 6.67% 45.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1002269285 A -> C LOC_Os10g04740.1 intron_variant ; MODIFIER silent_mutation Average:9.346; most accessible tissue: Callus, score: 19.884 N N N N
vg1002269285 A -> DEL N N silent_mutation Average:9.346; most accessible tissue: Callus, score: 19.884 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002269285 NA 8.75E-06 mr1272 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
vg1002269285 2.16E-06 NA mr1486 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
vg1002269285 9.60E-06 NA 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
vg1002269285 8.38E-06 NA 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
vg1002269285 4.67E-06 8.63E-06 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
vg1002269285 NA 4.09E-08 mr1709 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
vg1002269285 1.30E-06 NA mr1486_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
vg1002269285 4.66E-06 NA 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
vg1002269285 8.84E-06 NA 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
vg1002269285 NA 1.51E-16 mr1709_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
vg1002269285 NA 2.65E-11 mr1709_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
vg1002269285 NA 1.07E-09 mr1709_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