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Detailed information for vg0900381058:

Variant ID: vg0900381058 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 381058
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGTATGACGGCACCACTAACCCCGAATCGTGGCTTACCGTCTACGGTCTCGCAATCCGTGCAGCAGGAGGAGACAACAAGGCCATGGCGAATTATTTA[C/T]
CGGTGGCTTTAGCAGATTCCGCCCGATCTTGGCTCCATGGATTGCCCCGTGGTACAATTGGATCTTGGGCCGAACTACGCGACCACTTCATCGCCAACTT

Reverse complement sequence

AAGTTGGCGATGAAGTGGTCGCGTAGTTCGGCCCAAGATCCAATTGTACCACGGGGCAATCCATGGAGCCAAGATCGGGCGGAATCTGCTAAAGCCACCG[G/A]
TAAATAATTCGCCATGGCCTTGTTGTCTCCTCCTGCTGCACGGATTGCGAGACCGTAGACGGTAAGCCACGATTCGGGGTTAGTGGTGCCGTCATACTTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 31.40% 5.50% 6.90% 56.12% NA
All Indica  2759 12.50% 0.30% 6.27% 80.94% NA
All Japonica  1512 68.30% 15.90% 6.55% 9.19% NA
Aus  269 3.70% 0.00% 17.84% 78.44% NA
Indica I  595 17.00% 0.20% 3.19% 79.66% NA
Indica II  465 25.40% 0.20% 6.88% 67.53% NA
Indica III  913 3.40% 0.20% 6.24% 90.14% NA
Indica Intermediate  786 12.10% 0.50% 8.27% 79.13% NA
Temperate Japonica  767 76.40% 0.50% 7.95% 15.12% NA
Tropical Japonica  504 50.40% 43.10% 5.56% 0.99% NA
Japonica Intermediate  241 80.10% 8.30% 4.15% 7.47% NA
VI/Aromatic  96 46.90% 0.00% 2.08% 51.04% NA
Intermediate  90 58.90% 14.40% 4.44% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0900381058 C -> DEL LOC_Os09g01530.1 N frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0900381058 C -> T LOC_Os09g01530.1 missense_variant ; p.Pro436Ser; MODERATE nonsynonymous_codon ; P436S Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 benign 0.945 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0900381058 3.75E-08 NA Grain_weight All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0900381058 NA 1.72E-06 mr1248 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
vg0900381058 NA 8.08E-10 mr1533 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
vg0900381058 NA 7.89E-06 mr1602 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
vg0900381058 NA 1.34E-09 mr1980 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
vg0900381058 NA 2.41E-11 mr1097_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
vg0900381058 NA 2.99E-07 mr1206_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
vg0900381058 NA 9.53E-07 mr1277_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
vg0900381058 NA 5.71E-06 mr1425_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
vg0900381058 NA 1.51E-13 mr1742_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
vg0900381058 NA 5.36E-10 mr1769_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
vg0900381058 NA 2.94E-07 mr1786_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