| Variant ID: vg0324116929 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 24116929 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGATTTTGGAGAAGTTCTCGATGAACCTCCGGTAGTATCCTGCCAAACCCAAAAAGCTGCGAACCTGAGTAACTATCTTGGGTTGCTTCCAATCAGTGAC[A/G]
GCGGTTACTGTTTCGGGGTCCACAGCAACTCCTTTAGTGGATATCACGTGCCCTAAGAACTTGACTTCGGACAACCAGAACTCACACTTGCTGAGCTTGC
GCAAGCTCAGCAAGTGTGAGTTCTGGTTGTCCGAAGTCAAGTTCTTAGGGCACGTGATATCCACTAAAGGAGTTGCTGTGGACCCCGAAACAGTAACCGC[T/C]
GTCACTGATTGGAAGCAACCCAAGATAGTTACTCAGGTTCGCAGCTTTTTGGGTTTGGCAGGATACTACCGGAGGTTCATCGAGAACTTCTCCAAAATCG
| 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 | 41.20% | 25.10% | 12.17% | 21.50% | NA |
| All Indica | 2759 | 7.90% | 36.60% | 20.08% | 35.45% | NA |
| All Japonica | 1512 | 99.30% | 0.10% | 0.13% | 0.46% | NA |
| Aus | 269 | 40.50% | 55.00% | 1.12% | 3.35% | NA |
| Indica I | 595 | 10.80% | 13.10% | 23.87% | 52.27% | NA |
| Indica II | 465 | 7.50% | 20.90% | 30.97% | 40.65% | NA |
| Indica III | 913 | 2.60% | 61.70% | 11.39% | 24.32% | NA |
| Indica Intermediate | 786 | 12.00% | 34.60% | 20.87% | 32.57% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 76.00% | 14.60% | 7.29% | 2.08% | NA |
| Intermediate | 90 | 52.20% | 15.60% | 10.00% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0324116929 | A -> DEL | LOC_Os03g43250.1 | N | frameshift_variant | Average:11.677; most accessible tissue: Callus, score: 30.379 | N | N | N | N |
| vg0324116929 | A -> G | LOC_Os03g43250.1 | synonymous_variant ; p.Ala429Ala; LOW | synonymous_codon | Average:11.677; most accessible tissue: Callus, score: 30.379 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0324116929 | NA | 4.13E-12 | mr1744 | 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 |
| vg0324116929 | 4.14E-06 | 4.14E-06 | mr1187_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 |