| Variant ID: vg0222557366 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22557366 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 241. )
CAAAATATTGTCAAGGAGTTCTCCATCAAATCTGAGGAGCACAGACTGCAATCCTATCGACAAGAGCCGACTAGACGGTCTATACTCAACCCGAATGGAG[C/T]
CCTCAACTTGAATACTACTGCAAGTAGATTTGAAGAAAGTCTCCATACTCCAACTTGCCTTGAACATGCAAGAATTAGGATGGCGGCGACTGAACCCCTG
CAGGGGTTCAGTCGCCGCCATCCTAATTCTTGCATGTTCAAGGCAAGTTGGAGTATGGAGACTTTCTTCAAATCTACTTGCAGTAGTATTCAAGTTGAGG[G/A]
CTCCATTCGGGTTGAGTATAGACCGTCTAGTCGGCTCTTGTCGATAGGATTGCAGTCTGTGCTCCTCAGATTTGATGGAGAACTCCTTGACAATATTTTG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.30% | 47.70% | 1.31% | 0.66% | NA |
| All Indica | 2759 | 77.60% | 19.90% | 1.99% | 0.51% | NA |
| All Japonica | 1512 | 1.90% | 96.90% | 0.20% | 1.06% | NA |
| Aus | 269 | 69.50% | 29.40% | 1.12% | 0.00% | NA |
| Indica I | 595 | 73.80% | 23.50% | 1.68% | 1.01% | NA |
| Indica II | 465 | 92.50% | 6.00% | 0.65% | 0.86% | NA |
| Indica III | 913 | 70.00% | 26.80% | 3.07% | 0.11% | NA |
| Indica Intermediate | 786 | 80.50% | 17.30% | 1.78% | 0.38% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 4.40% | 92.10% | 0.60% | 2.98% | NA |
| Japonica Intermediate | 241 | 0.80% | 98.80% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 1.00% | 97.90% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 23.30% | 75.60% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0222557366 | C -> T | LOC_Os02g37309.1 | missense_variant ; p.Gly124Asp; MODERATE | nonsynonymous_codon ; G124D | Average:50.269; most accessible tissue: Zhenshan97 panicle, score: 80.486 | unknown | unknown | TOLERATED | 1.00 |
| vg0222557366 | C -> DEL | LOC_Os02g37309.1 | N | frameshift_variant | Average:50.269; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0222557366 | NA | 1.38E-07 | mr1222 | 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 |
| vg0222557366 | 3.60E-06 | NA | mr1913 | 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 |
| vg0222557366 | NA | 8.38E-07 | mr1561_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 |
| vg0222557366 | NA | 5.33E-07 | mr1875_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 |
| vg0222557366 | 4.75E-07 | 6.59E-09 | mr1908_2 | 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 |
| vg0222557366 | NA | 1.02E-06 | mr1996_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 |