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Detailed information for vg0817588459:

Variant ID: vg0817588459 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17588459
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCGCCGCTTATATGGCCCGCCTGCAAAGATGCCCCTATATAGTCTTCGTACTCCCCGAGCCCTGTTCATTCTCCCCGAAGTTTCTCTCTCCTAAAGTGT[C/G]
TTAAATATAGGGGGGAGGTTTTGAACTTCAAATCTTCGGGGGATTTTTTTACAGTGCTTAGATCTACTCATTTCCACCCTAGGTATGCATTTTTTTTAAG

Reverse complement sequence

CTTAAAAAAAATGCATACCTAGGGTGGAAATGAGTAGATCTAAGCACTGTAAAAAAATCCCCCGAAGATTTGAAGTTCAAAACCTCCCCCCTATATTTAA[G/C]
ACACTTTAGGAGAGAGAAACTTCGGGGAGAATGAACAGGGCTCGGGGAGTACGAAGACTATATAGGGGCATCTTTGCAGGCGGGCCATATAAGCGGCGCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.40% 5.40% 0.06% 0.21% NA
All Indica  2759 97.40% 2.40% 0.00% 0.18% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 32.00% 65.10% 1.12% 1.86% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 97.50% 2.30% 0.00% 0.22% NA
Indica Intermediate  786 95.50% 4.10% 0.00% 0.38% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0817588459 C -> G LOC_Os08g28750.1 intron_variant ; MODIFIER silent_mutation Average:57.581; most accessible tissue: Minghui63 young leaf, score: 76.82 N N N N
vg0817588459 C -> DEL N N silent_mutation Average:57.581; most accessible tissue: Minghui63 young leaf, score: 76.82 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817588459 NA 4.65E-08 mr1836 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
vg0817588459 8.02E-06 NA mr1040_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
vg0817588459 1.85E-06 NA mr1581_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
vg0817588459 3.58E-06 NA mr1836_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