| Variant ID: vg0527609874 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 27609874 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 236. )
TGCCGTTACTGTGGCAAACTTGGTCACTGGGCCAAGGACTGTCGCAAGGCGAAGCGAGACCGCGAGAAGCTGGCTCAAGCAAATCTTCTCATCGCTGAGC[C/T]
AGCTCACCCCGCGGACGAAGGGGAGCCGACACTCCTGATGGCGCAAGTGTGCGAGCTTGCCCCTGCTACCGATTCTGTCATTACTGATGGGGAGGTGACA
TGTCACCTCCCCATCAGTAATGACAGAATCGGTAGCAGGGGCAAGCTCGCACACTTGCGCCATCAGGAGTGTCGGCTCCCCTTCGTCCGCGGGGTGAGCT[G/A]
GCTCAGCGATGAGAAGATTTGCTTGAGCCAGCTTCTCGCGGTCTCGCTTCGCCTTGCGACAGTCCTTGGCCCAGTGACCAAGTTTGCCACAGTAACGGCA
| 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 | 91.60% | 7.60% | 0.13% | 0.72% | NA |
| All Indica | 2759 | 93.30% | 6.20% | 0.11% | 0.33% | NA |
| All Japonica | 1512 | 88.60% | 10.10% | 0.20% | 1.06% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.50% | 3.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 88.40% | 11.00% | 0.00% | 0.65% | NA |
| Indica III | 913 | 95.30% | 4.30% | 0.11% | 0.33% | NA |
| Indica Intermediate | 786 | 91.60% | 7.80% | 0.25% | 0.38% | NA |
| Temperate Japonica | 767 | 98.60% | 1.30% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 81.20% | 15.50% | 0.40% | 2.98% | NA |
| Japonica Intermediate | 241 | 72.60% | 27.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 63.50% | 29.20% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 91.10% | 6.70% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0527609874 | C -> T | LOC_Os05g48170.1 | missense_variant ; p.Pro246Leu; MODERATE | nonsynonymous_codon ; P246L | Average:63.015; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | unknown | unknown | TOLERATED | 0.20 |
| vg0527609874 | C -> DEL | LOC_Os05g48170.1 | N | frameshift_variant | Average:63.015; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0527609874 | NA | 7.74E-06 | mr1088 | 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 |
| vg0527609874 | NA | 4.74E-06 | mr1103 | 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 |
| vg0527609874 | 5.88E-06 | 5.37E-06 | mr1245 | 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 |
| vg0527609874 | 1.84E-06 | 3.10E-07 | mr1261 | 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 |
| vg0527609874 | NA | 8.59E-07 | mr1437 | 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 |
| vg0527609874 | NA | 3.61E-07 | mr1088_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 |
| vg0527609874 | NA | 2.98E-06 | mr1246_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 |