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

Detailed information for vg0909993670:

Variant ID: vg0909993670 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 9993670
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


AGTCTCGCCAAAGAAAGGGGTCTCGTTGAATCAGATTGAGACGGAAATCCCAGTGGACACCGTAGAGAAGAACTTGAGAAAATTGGAAGATATACCCATA[A/G]
TCTGCGAGTATCCAGAAGTGTTCCCCGAAGACCTCACTACCATGCCACCCAAGAGAGAGATTGAATTCCGGATTGACTTGGCACCGGGAACTGCTCCAAT

Reverse complement sequence

ATTGGAGCAGTTCCCGGTGCCAAGTCAATCCGGAATTCAATCTCTCTCTTGGGTGGCATGGTAGTGAGGTCTTCGGGGAACACTTCTGGATACTCGCAGA[T/C]
TATGGGTATATCTTCCAATTTTCTCAAGTTCTTCTCTACGGTGTCCACTGGGATTTCCGTCTCAATCTGATTCAACGAGACCCCTTTCTTTGGCGAGACT

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 73.50% 25.00% 1.10% 0.44% NA
All Indica  2759 93.90% 5.20% 0.87% 0.00% NA
All Japonica  1512 34.10% 63.20% 1.39% 1.39% NA
Aus  269 85.50% 13.40% 1.12% 0.00% NA
Indica I  595 84.40% 13.80% 1.85% 0.00% NA
Indica II  465 94.20% 4.50% 1.29% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 94.40% 4.70% 0.89% 0.00% NA
Temperate Japonica  767 4.70% 94.50% 0.65% 0.13% NA
Tropical Japonica  504 84.50% 10.30% 1.98% 3.17% NA
Japonica Intermediate  241 22.00% 73.90% 2.49% 1.66% NA
VI/Aromatic  96 75.00% 22.90% 2.08% 0.00% NA
Intermediate  90 71.10% 26.70% 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
vg0909993670 A -> G LOC_Os09g16350.1 missense_variant ; p.Ile552Val; MODERATE nonsynonymous_codon ; I552V Average:20.783; most accessible tissue: Minghui63 flower, score: 32.19 unknown unknown TOLERATED 1.00
vg0909993670 A -> DEL LOC_Os09g16350.1 N frameshift_variant Average:20.783; most accessible tissue: Minghui63 flower, score: 32.19 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909993670 NA 9.28E-06 mr1047 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
vg0909993670 NA 7.35E-07 mr1271 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
vg0909993670 NA 4.26E-08 mr1425 Jap_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
vg0909993670 NA 1.66E-11 mr1471 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
vg0909993670 NA 2.15E-06 mr1471 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
vg0909993670 NA 6.38E-06 mr1530 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
vg0909993670 NA 3.97E-06 mr1642 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
vg0909993670 NA 2.10E-20 mr1679 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
vg0909993670 NA 1.17E-08 mr1679 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
vg0909993670 NA 9.93E-09 mr1693 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
vg0909993670 NA 8.08E-10 mr1712 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
vg0909993670 NA 1.64E-06 mr1815 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
vg0909993670 NA 1.33E-06 mr1250_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
vg0909993670 NA 5.41E-17 mr1539_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
vg0909993670 NA 1.82E-22 mr1679_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
vg0909993670 NA 3.57E-07 mr1679_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