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Detailed information for vg0907029568:

Variant ID: vg0907029568 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7029568
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, C: 0.35, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTCTGGATTGAGCATGAGGCGATATTGTCGGAGGTTGTCGAACGTTTCCCGCAGATCGTCAATCAATGAGTCGCTTGTCTTGGTCTTGACAACGATAT[T/C]
GTCGACGTAGGCGTCGACATTGTTGCTGAGCTGGTCGCTAAGTGCGCACTGGACCGTGCGCTGGAAAGTATTCCCTGCGGTTATTAGTCCGAACGGCATC

Reverse complement sequence

GATGCCGTTCGGACTAATAACCGCAGGGAATACTTTCCAGCGCACGGTCCAGTGCGCACTTAGCGACCAGCTCAGCAACAATGTCGACGCCTACGTCGAC[A/G]
ATATCGTTGTCAAGACCAAGACAAGCGACTCATTGATTGACGATCTGCGGGAAACGTTCGACAACCTCCGACAATATCGCCTCATGCTCAATCCAGAGAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 26.30% 6.10% 15.13% 52.39% NA
All Indica  2759 1.80% 1.30% 15.80% 81.04% NA
All Japonica  1512 75.30% 15.70% 8.07% 0.99% NA
Aus  269 0.40% 2.20% 26.77% 70.63% NA
Indica I  595 2.50% 0.30% 5.04% 92.10% NA
Indica II  465 0.60% 3.40% 9.89% 86.02% NA
Indica III  913 0.50% 0.40% 31.54% 67.47% NA
Indica Intermediate  786 3.60% 1.80% 9.16% 85.50% NA
Temperate Japonica  767 92.40% 5.00% 1.96% 0.65% NA
Tropical Japonica  504 63.10% 19.60% 15.67% 1.59% NA
Japonica Intermediate  241 46.10% 41.50% 11.62% 0.83% NA
VI/Aromatic  96 21.90% 5.20% 68.75% 4.17% NA
Intermediate  90 37.80% 6.70% 21.11% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0907029568 T -> DEL LOC_Os09g12330.1 N frameshift_variant Average:18.83; most accessible tissue: Callus, score: 29.521 N N N N
vg0907029568 T -> C LOC_Os09g12330.1 missense_variant ; p.Asn406Asp; MODERATE nonsynonymous_codon Average:18.83; most accessible tissue: Callus, score: 29.521 benign -0.587 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907029568 8.31E-08 NA mr1092 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
vg0907029568 NA 8.78E-21 mr1102 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
vg0907029568 NA 5.62E-19 mr1114 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
vg0907029568 NA 3.42E-18 mr1116 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
vg0907029568 7.61E-06 NA mr1120 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
vg0907029568 NA 1.56E-07 mr1190 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
vg0907029568 NA 1.85E-15 mr1361 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
vg0907029568 NA 5.97E-26 mr1917 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
vg0907029568 NA 7.36E-18 mr1114_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
vg0907029568 NA 8.43E-06 mr1114_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
vg0907029568 NA 9.54E-08 mr1700_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
vg0907029568 NA 9.38E-06 mr1840_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