| Variant ID: vg1218421558 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18421558 |
| 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: 116. )
AAGCCTCCGTCGCCACCGCTCAAGCTCAAGCACAAGTTCAAGTTGCCGAACCACCTCCCCTCTCTGTTCGCCAGTCTCAGTCGGCGATCCAAGGACAGCC[G/A]
CCAAGGCAAGGCCAGGCCCCCCATAACTTGGAGAAAGTTCAGAACAGACCGTGCGGGCAAAGCTGTGATGGCGGTCGAAGAAGTGCAAGCCCTCCGCAAG
CTTGCGGAGGGCTTGCACTTCTTCGACCGCCATCACAGCTTTGCCCGCACGGTCTGTTCTGAACTTTCTCCAAGTTATGGGGGGCCTGGCCTTGCCTTGG[C/T]
GGCTGTCCTTGGATCGCCGACTGAGACTGGCGAACAGAGAGGGGAGGTGGTTCGGCAACTTGAACTTGTGCTTGAGCTTGAGCGGTGGCGACGGAGGCTT
| 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 | 91.30% | 2.20% | 2.37% | 4.13% | NA |
| All Indica | 2759 | 88.00% | 1.00% | 3.99% | 7.00% | NA |
| All Japonica | 1512 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 68.70% | 1.30% | 9.58% | 20.34% | NA |
| Indica II | 465 | 97.00% | 0.90% | 0.86% | 1.29% | NA |
| Indica III | 913 | 95.60% | 0.80% | 1.97% | 1.64% | NA |
| Indica Intermediate | 786 | 88.50% | 1.00% | 3.94% | 6.49% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 79.30% | 20.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 2.22% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218421558 | G -> DEL | LOC_Os12g30670.1 | N | frameshift_variant | Average:33.047; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg1218421558 | G -> A | LOC_Os12g30670.1 | synonymous_variant ; p.Pro317Pro; LOW | synonymous_codon | Average:33.047; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1218421558 | 2.62E-06 | 2.62E-06 | mr1356 | 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 |
| vg1218421558 | NA | 2.34E-06 | mr1460 | 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 |