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Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0905075837:

Variant ID: vg0905075837 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5075837
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATCTAGTGTGTGTTGTAACGCCCCGATTTTCGTTCGGGTTTTAAAATCATTTAATAATGCATTTCAAGAAATTATATTAAAAGTTAAAGCAATTTATTC[G/A]
AGTGAATTAATGGGAGAATTAAAATTTTCCCTTAAAAATCATTGGCCGGGAATATTTTGCAATATTCTTTTGCCCTAAAATACTCTCTGAAATTTCCTGT

Reverse complement sequence

ACAGGAAATTTCAGAGAGTATTTTAGGGCAAAAGAATATTGCAAAATATTCCCGGCCAATGATTTTTAAGGGAAAATTTTAATTCTCCCATTAATTCACT[C/T]
GAATAAATTGCTTTAACTTTTAATATAATTTCTTGAAATGCATTATTAAATGATTTTAAAACCCGAACGAAAATCGGGGCGTTACAACACACACTAGATC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.70% 8.10% 1.99% 1.29% NA
All Indica  2759 91.90% 7.50% 0.62% 0.00% NA
All Japonica  1512 91.50% 0.20% 4.30% 3.97% NA
Aus  269 38.30% 61.00% 0.74% 0.00% NA
Indica I  595 95.50% 4.40% 0.17% 0.00% NA
Indica II  465 92.70% 7.30% 0.00% 0.00% NA
Indica III  913 94.00% 5.90% 0.11% 0.00% NA
Indica Intermediate  786 86.40% 11.70% 1.91% 0.00% NA
Temperate Japonica  767 85.80% 0.00% 7.43% 6.78% NA
Tropical Japonica  504 99.20% 0.40% 0.00% 0.40% NA
Japonica Intermediate  241 93.80% 0.40% 3.32% 2.49% NA
VI/Aromatic  96 84.40% 5.20% 10.42% 0.00% NA
Intermediate  90 95.60% 3.30% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0905075837 G -> DEL N N silent_mutation Average:37.705; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0905075837 G -> A LOC_Os09g09430.1 intron_variant ; MODIFIER silent_mutation Average:37.705; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905075837 NA 1.61E-07 mr1236_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
vg0905075837 7.82E-06 4.74E-08 mr1252_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
vg0905075837 NA 6.58E-06 mr1306_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
vg0905075837 NA 5.22E-06 mr1381_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
vg0905075837 NA 3.22E-07 mr1597_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
vg0905075837 NA 8.35E-06 mr1704_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
vg0905075837 NA 3.85E-06 mr1743_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
vg0905075837 3.45E-06 NA mr1783_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
vg0905075837 5.83E-06 NA mr1804_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
vg0905075837 7.11E-06 NA mr1844_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
vg0905075837 1.23E-07 NA mr1874_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
vg0905075837 9.19E-06 9.18E-06 mr1953_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