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Detailed information for vg0907770893:

Variant ID: vg0907770893 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7770893
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.29, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


TCCGCAGCCCAACATGACTGTACTCCTACTCTGTAATAAAGAGACCTCTGTTGCTGTGATATTCTGTCTTCCTGTGATACCAGCACTGTTTCCTGGGACT[A/G]
ATATCGATAAACAGGTTAATTTGGAGCGTCACGGGCTAGTTCCGTTCGGGGCTAGTTCGGGGCATGACACCCTGGCAATGCGTAGATACACAGGGCCGAG

Reverse complement sequence

CTCGGCCCTGTGTATCTACGCATTGCCAGGGTGTCATGCCCCGAACTAGCCCCGAACGGAACTAGCCCGTGACGCTCCAAATTAACCTGTTTATCGATAT[T/C]
AGTCCCAGGAAACAGTGCTGGTATCACAGGAAGACAGAATATCACAGCAACAGAGGTCTCTTTATTACAGAGTAGGAGTACAGTCATGTTGGGCTGCGGA

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 52.60% 21.50% 4.93% 21.03% NA
All Indica  2759 79.40% 2.90% 7.50% 10.18% NA
All Japonica  1512 2.10% 60.10% 0.86% 36.90% NA
Aus  269 82.50% 0.00% 0.74% 16.73% NA
Indica I  595 68.70% 3.20% 13.45% 14.62% NA
Indica II  465 81.10% 1.30% 9.46% 8.17% NA
Indica III  913 86.90% 1.60% 3.07% 8.43% NA
Indica Intermediate  786 78.00% 5.00% 7.00% 10.05% NA
Temperate Japonica  767 2.90% 78.40% 0.26% 18.51% NA
Tropical Japonica  504 1.20% 25.40% 1.79% 71.63% NA
Japonica Intermediate  241 1.70% 74.70% 0.83% 22.82% NA
VI/Aromatic  96 5.20% 1.00% 2.08% 91.67% NA
Intermediate  90 36.70% 28.90% 10.00% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0907770893 A -> G LOC_Os09g13430.1 missense_variant ; p.Asn30Asp; MODERATE nonsynonymous_codon Average:15.146; most accessible tissue: Zhenshan97 root, score: 22.162 unknown unknown DELETERIOUS 0.00
vg0907770893 A -> DEL LOC_Os09g13430.1 N frameshift_variant Average:15.146; most accessible tissue: Zhenshan97 root, score: 22.162 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907770893 NA 1.69E-14 mr1062 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
vg0907770893 NA 1.81E-23 mr1102 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
vg0907770893 NA 4.04E-10 mr1198 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
vg0907770893 NA 1.05E-10 mr1307 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
vg0907770893 NA 9.27E-10 mr1322 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
vg0907770893 NA 4.83E-17 mr1323 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
vg0907770893 NA 1.45E-09 mr1336 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
vg0907770893 NA 4.04E-09 mr1442 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
vg0907770893 NA 8.30E-07 mr1527 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
vg0907770893 NA 6.62E-13 mr1579 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
vg0907770893 NA 4.59E-07 mr1646 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
vg0907770893 NA 1.08E-06 mr1781 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
vg0907770893 NA 5.66E-09 mr1866 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
vg0907770893 NA 2.83E-14 mr1940 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
vg0907770893 NA 1.28E-06 mr1020_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
vg0907770893 NA 4.78E-16 mr1162_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