Search for Variation information by Variation ID:
Detailed information for vg0913511852:
| Variant ID: vg0913511852 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 13511852 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 100. )
Flanking Sequence (100 bp) in Reference Genome:
AAGGTTTCTTCTAGATCCGAGATTAAATCATCCTTCTGCTTAGTCTTGACGACTACATCATCCACGTACGCTTCGACATTGCGGCTAATTTGCATCGAGA[A/G]
GCATCTCTGAATCATACGTTGATAAGTTGCTCCTGCATTTTTTAGTCCGAATGGCATGGTGATGTAGCAATAGGCCCCGAAGGGTGTGATGAATGAAGTC
Reverse complement sequence
GACTTCATTCATCACACCCTTCGGGGCCTATTGCTACATCACCATGCCATTCGGACTAAAAAATGCAGGAGCAACTTATCAACGTATGATTCAGAGATGC[T/C]
TCTCGATGCAAATTAGCCGCAATGTCGAAGCGTACGTGGATGATGTAGTCGTCAAGACTAAGCAGAAGGATGATTTAATCTCGGATCTAGAAGAAACCTT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.40% | 5.30% | 5.35% | 5.95% | NA |
| All Indica | 2759 | 75.50% | 8.80% | 8.23% | 7.47% | NA |
| All Japonica | 1512 | 96.10% | 0.10% | 0.79% | 3.04% | NA |
| Aus | 269 | 93.30% | 0.40% | 1.86% | 4.46% | NA |
| Indica I | 595 | 78.80% | 4.20% | 8.24% | 8.74% | NA |
| Indica II | 465 | 88.20% | 3.00% | 6.67% | 2.15% | NA |
| Indica III | 913 | 66.80% | 16.50% | 7.34% | 9.31% | NA |
| Indica Intermediate | 786 | 75.60% | 6.70% | 10.18% | 7.51% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.39% | 0.78% | NA |
| Tropical Japonica | 504 | 91.30% | 0.20% | 1.79% | 6.75% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 3.12% | 13.54% | NA |
| Intermediate | 90 | 84.40% | 4.40% | 6.67% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0913511852 | A -> G | LOC_Os09g22360.1 | missense_variant ; p.Phe1006Leu; MODERATE | nonsynonymous_codon ; F1006L | Average:19.352; most accessible tissue: Minghui63 young leaf, score: 49.581 | benign  |
0.312 |
TOLERATED | 0.20 |
| vg0913511852 | A -> DEL | LOC_Os09g22360.1 | N | frameshift_variant | Average:19.352; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0913511852 | NA | 1.67E-08 | mr1037 | Ind_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 |
| vg0913511852 | 3.58E-06 | 3.58E-06 | mr1370 | Ind_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 |
| vg0913511852 | NA | 5.17E-06 | mr1037_2 | Ind_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 |