| Variant ID: vg0907659025 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 7659025 |
| Reference Allele: C | Alternative Allele: T,CGG |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACAGAGTAAAGCAAGCATGTGGCACCCCTCTCTATTTCACTCTAGCTTCGCCCGTGTGTTGTCCATGTAGAGATTGCAAGAATAAGAATATGTTTGAAAG[C/T,CGG]
AGAGTGGACGATTTACACTCTCACTTGATACAACGGGGATTTATGAAGGGATACACATGTTGGGCGAAGCATGGAGAGCAAGAATTGGGAAGTGGTGCAG
CTGCACCACTTCCCAATTCTTGCTCTCCATGCTTCGCCCAACATGTGTATCCCTTCATAAATCCCCGTTGTATCAAGTGAGAGTGTAAATCGTCCACTCT[G/A,CCG]
CTTTCAAACATATTCTTATTCTTGCAATCTCTACATGGACAACACACGGGCGAAGCTAGAGTGAAATAGAGAGGGGTGCCACATGCTTGCTTTACTCTGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.70% | 14.80% | 1.97% | 56.43% | CGG: 0.11% |
| All Indica | 2759 | 10.80% | 5.80% | 2.43% | 80.86% | CGG: 0.14% |
| All Japonica | 1512 | 57.10% | 29.40% | 1.12% | 12.37% | NA |
| Aus | 269 | 13.40% | 1.90% | 2.97% | 81.41% | CGG: 0.37% |
| Indica I | 595 | 6.60% | 5.20% | 6.22% | 82.02% | NA |
| Indica II | 465 | 6.70% | 2.60% | 2.37% | 87.96% | CGG: 0.43% |
| Indica III | 913 | 15.70% | 6.80% | 0.33% | 77.00% | CGG: 0.22% |
| Indica Intermediate | 786 | 10.80% | 6.90% | 2.04% | 80.28% | NA |
| Temperate Japonica | 767 | 66.40% | 9.80% | 1.96% | 21.90% | NA |
| Tropical Japonica | 504 | 34.50% | 63.70% | 0.40% | 1.39% | NA |
| Japonica Intermediate | 241 | 74.70% | 20.30% | 0.00% | 4.98% | NA |
| VI/Aromatic | 96 | 34.40% | 61.50% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 36.70% | 33.30% | 1.11% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0907659025 | C -> DEL | LOC_Os09g13280.1 | N | frameshift_variant | Average:15.188; most accessible tissue: Callus, score: 53.631 | N | N | N | N |
| vg0907659025 | C -> T | LOC_Os09g13280.1 | synonymous_variant ; p.Ser62Ser; LOW | synonymous_codon | Average:15.188; most accessible tissue: Callus, score: 53.631 | N | N | N | N |
| vg0907659025 | C -> CGG | LOC_Os09g13280.1 | frameshift_variant ; p.Arg63fs; HIGH | frameshift_variant | Average:15.188; most accessible tissue: Callus, score: 53.631 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0907659025 | NA | 3.89E-07 | mr1002 | 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 |
| vg0907659025 | NA | 4.36E-11 | mr1070 | 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 |
| vg0907659025 | NA | 6.44E-11 | mr1128 | 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 |
| vg0907659025 | NA | 1.14E-06 | mr1438 | 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 |
| vg0907659025 | NA | 5.42E-08 | mr1002_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 |
| vg0907659025 | NA | 8.11E-07 | mr1057_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 |
| vg0907659025 | NA | 2.30E-09 | mr1438_2 | 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 |