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Detailed information for vg0717004102:

Variant ID: vg0717004102 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 17004102
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCCATCGCGAAATCCCCGATTCGCCCTAAAAAATCCTCTCCCGCCGCAGCTAATCTCCTCCTCCCGCCACCTATTCGTCCGCTCCACCGATATCCCAAG[A/G]
TTTCCCCAATCAAATCCACGCATGTTAATCATGAACCAAAAGAAATCAAGGTGGGGAAACAAATCAAGAACCCAAAGAAATCAAGGTGGTGCAAACAAAT

Reverse complement sequence

ATTTGTTTGCACCACCTTGATTTCTTTGGGTTCTTGATTTGTTTCCCCACCTTGATTTCTTTTGGTTCATGATTAACATGCGTGGATTTGATTGGGGAAA[T/C]
CTTGGGATATCGGTGGAGCGGACGAATAGGTGGCGGGAGGAGGAGATTAGCTGCGGCGGGAGAGGATTTTTTAGGGCGAATCGGGGATTTCGCGATGGGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.50% 3.80% 0.70% 0.00% NA
All Indica  2759 98.70% 0.40% 0.98% 0.00% NA
All Japonica  1512 99.50% 0.10% 0.40% 0.00% NA
Aus  269 37.50% 62.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 95.50% 1.10% 3.31% 0.00% NA
Temperate Japonica  767 99.20% 0.00% 0.78% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0717004102 A -> G LOC_Os07g28980.1 intron_variant ; MODIFIER silent_mutation Average:54.135; most accessible tissue: Minghui63 flag leaf, score: 79.383 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0717004102 2.70E-08 2.32E-49 mr1549 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
vg0717004102 4.22E-09 8.60E-58 mr1550 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
vg0717004102 6.02E-11 1.28E-56 mr1757 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
vg0717004102 NA 2.34E-18 mr1240_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
vg0717004102 9.68E-06 NA mr1242_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
vg0717004102 NA 8.93E-13 mr1409_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
vg0717004102 NA 2.95E-08 mr1510_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
vg0717004102 1.56E-08 3.14E-47 mr1549_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
vg0717004102 9.80E-10 2.52E-69 mr1550_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
vg0717004102 8.99E-10 8.32E-43 mr1757_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
vg0717004102 NA 5.73E-07 mr1762_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