| Variant ID: vg0327981223 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27981223 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 123. )
GGAGCACCTGACGACGTACACGCGGATGGTGGAGTCGATGCGCTCGATTCTCCGAGTGCTCACCTGTCGTGCAGACAACGTTACTCGGGCAGACGCAGCT[G/A]
TACAGCGGCCACCCGTACCGACTGGTCCCCGTCCAACTGCGCACGTTCCTAGGCCGACTCCCCCTCCGCACGGAGGTAAGTATTTTTAAGGATTTTTCTA
TAGAAAAATCCTTAAAAATACTTACCTCCGTGCGGAGGGGGAGTCGGCCTAGGAACGTGCGCAGTTGGACGGGGACCAGTCGGTACGGGTGGCCGCTGTA[C/T]
AGCTGCGTCTGCCCGAGTAACGTTGTCTGCACGACAGGTGAGCACTCGGAGAATCGAGCGCATCGACTCCACCATCCGCGTGTACGTCGTCAGGTGCTCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.90% | 0.30% | 8.21% | 39.59% | NA |
| All Indica | 2759 | 31.20% | 0.40% | 5.04% | 63.28% | NA |
| All Japonica | 1512 | 98.10% | 0.00% | 0.86% | 1.06% | NA |
| Aus | 269 | 8.20% | 0.00% | 60.22% | 31.60% | NA |
| Indica I | 595 | 13.80% | 0.50% | 2.02% | 83.70% | NA |
| Indica II | 465 | 54.20% | 0.20% | 4.09% | 41.51% | NA |
| Indica III | 913 | 27.20% | 0.40% | 7.67% | 64.73% | NA |
| Indica Intermediate | 786 | 35.60% | 0.50% | 4.83% | 59.03% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 2.18% | 1.79% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.83% | 1.66% | NA |
| VI/Aromatic | 96 | 33.30% | 0.00% | 63.54% | 3.12% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 14.44% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0327981223 | G -> A | LOC_Os03g49120.1 | synonymous_variant ; p.Leu1398Leu; LOW | synonymous_codon | Average:35.783; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 | N | N | N | N |
| vg0327981223 | G -> DEL | LOC_Os03g49120.1 | N | frameshift_variant | Average:35.783; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0327981223 | 6.33E-06 | 6.33E-06 | mr1294 | 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 |
| vg0327981223 | NA | 8.30E-06 | mr1507 | 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 |
| vg0327981223 | NA | 3.16E-06 | mr1537 | 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 |
| vg0327981223 | 7.92E-06 | 7.92E-06 | mr1972 | 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 |