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Detailed information for vg0702669541:

Variant ID: vg0702669541 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 2669541
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTAGAATGCTTATATTTAGAAACAGAGATACGGAGGGAGCTAGTACTACTAAAACAAGTACAGTATTCTGTACTAATTCCTCATTCTTATACAGATGAC[C/G]
TTGTTTAAACACGTACGTACATGTGGTATGGATTTTGAAATTTGCCCCACTAAAATTAAGATGTCAATTTTTTAAAAAATTTTGATTTATAAAATGATAA

Reverse complement sequence

TTATCATTTTATAAATCAAAATTTTTTAAAAAATTGACATCTTAATTTTAGTGGGGCAAATTTCAAAATCCATACCACATGTACGTACGTGTTTAAACAA[G/C]
GTCATCTGTATAAGAATGAGGAATTAGTACAGAATACTGTACTTGTTTTAGTAGTACTAGCTCCCTCCGTATCTCTGTTTCTAAATATAAGCATTCTAGA

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 83.40% 15.70% 0.91% 0.00% NA
All Indica  2759 98.80% 0.90% 0.29% 0.00% NA
All Japonica  1512 51.20% 46.60% 2.18% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.50% 2.40% 1.18% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 17.60% 79.80% 2.61% 0.00% NA
Tropical Japonica  504 95.40% 3.20% 1.39% 0.00% NA
Japonica Intermediate  241 65.60% 32.00% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 10.00% 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
vg0702669541 C -> G LOC_Os07g05620-LOC_Os07g05630 intergenic_region ; MODIFIER silent_mutation Average:34.771; most accessible tissue: Callus, score: 59.939 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0702669541 NA 1.53E-06 mr1543 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
vg0702669541 NA 1.71E-06 mr1648 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
vg0702669541 NA 4.95E-13 mr1879 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
vg0702669541 NA 8.79E-06 mr1195_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
vg0702669541 2.73E-07 NA mr1546_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
vg0702669541 NA 6.06E-06 mr1546_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