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Detailed information for vg1012949570:

Variant ID: vg1012949570 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 12949570
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTTTTAAACTAAACATTTGAGAATTAGTAATGGTTAGAACTTTAGAAGTTTAATGAAATATTAACTTAAGCGTTTTTTTTATCAGAGGAAGTTGTCAA[C/T]
AAAGATAACACGGGTTGATTACTCCCTTATTGATAGAGATAGCCTCCATTTTATAGCACAAAAGATTAGGGGTTGCCCCTCTTTCACGATGTCGACGTTT

Reverse complement sequence

AAACGTCGACATCGTGAAAGAGGGGCAACCCCTAATCTTTTGTGCTATAAAATGGAGGCTATCTCTATCAATAAGGGAGTAATCAACCCGTGTTATCTTT[G/A]
TTGACAACTTCCTCTGATAAAAAAAACGCTTAAGTTAATATTTCATTAAACTTCTAAAGTTCTAACCATTACTAATTCTCAAATGTTTAGTTTAAAAAAA

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 61.50% 38.50% 0.00% 0.00% NA
All Indica  2759 97.30% 2.70% 0.00% 0.00% NA
All Japonica  1512 9.80% 90.20% 0.00% 0.00% NA
Aus  269 9.70% 90.30% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 97.80% 2.20% 0.00% 0.00% NA
Indica Intermediate  786 95.20% 4.80% 0.00% 0.00% NA
Temperate Japonica  767 2.70% 97.30% 0.00% 0.00% NA
Tropical Japonica  504 17.30% 82.70% 0.00% 0.00% NA
Japonica Intermediate  241 16.60% 83.40% 0.00% 0.00% NA
VI/Aromatic  96 12.50% 87.50% 0.00% 0.00% NA
Intermediate  90 41.10% 58.90% 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
vg1012949570 C -> T LOC_Os10g25110.1 upstream_gene_variant ; 2822.0bp to feature; MODIFIER silent_mutation Average:28.824; most accessible tissue: Callus, score: 59.534 N N N N
vg1012949570 C -> T LOC_Os10g25110-LOC_Os10g25120 intergenic_region ; MODIFIER silent_mutation Average:28.824; most accessible tissue: Callus, score: 59.534 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1012949570 NA 7.66E-06 mr1450 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
vg1012949570 NA 3.04E-19 mr1627 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
vg1012949570 6.23E-08 NA mr1668 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
vg1012949570 NA 3.22E-23 mr1943 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
vg1012949570 NA 8.14E-36 mr1223_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
vg1012949570 NA 7.77E-07 mr1275_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
vg1012949570 6.85E-06 NA mr1438_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
vg1012949570 NA 2.37E-14 mr1575_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
vg1012949570 5.47E-06 1.66E-08 mr1668_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
vg1012949570 NA 3.80E-22 mr1698_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
vg1012949570 NA 3.06E-07 mr1885_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