| Variant ID: vg0430344329 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30344329 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 145. )
TGAACTGTTGTCCTTGAAAAATAACCAACATTTCTCGGATTTACAGATGCCTTGACTTTGAATACTGAAACTTCATCGGTCCATCAAATTGAAGCAATGG[C/T]
GATGCACCTTCATCCCGACAAGATTTGGAACTTAACCCTTAGTTGATGATAGGAAATTCCACATAAAAGTGACTCTCATTTAGCTCATGAACACACTGAC
GTCAGTGTGTTCATGAGCTAAATGAGAGTCACTTTTATGTGGAATTTCCTATCATCAACTAAGGGTTAAGTTCCAAATCTTGTCGGGATGAAGGTGCATC[G/A]
CCATTGCTTCAATTTGATGGACCGATGAAGTTTCAGTATTCAAAGTCAAGGCATCTGTAAATCCGAGAAATGTTGGTTATTTTTCAAGGACAACAGTTCA
| 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 | 72.00% | 5.60% | 20.80% | 1.52% | NA |
| All Indica | 2759 | 58.40% | 6.80% | 33.45% | 1.38% | NA |
| All Japonica | 1512 | 90.40% | 5.00% | 2.38% | 2.18% | NA |
| Aus | 269 | 96.30% | 0.00% | 3.35% | 0.37% | NA |
| Indica I | 595 | 49.70% | 4.00% | 44.71% | 1.51% | NA |
| Indica II | 465 | 51.40% | 6.70% | 39.78% | 2.15% | NA |
| Indica III | 913 | 68.60% | 7.20% | 23.44% | 0.77% | NA |
| Indica Intermediate | 786 | 57.10% | 8.50% | 32.82% | 1.53% | NA |
| Temperate Japonica | 767 | 97.40% | 0.70% | 1.17% | 0.78% | NA |
| Tropical Japonica | 504 | 78.40% | 13.90% | 4.76% | 2.98% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.40% | 1.24% | 4.98% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 3.30% | 15.56% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430344329 | C -> DEL | N | N | silent_mutation | Average:13.082; most accessible tissue: Minghui63 young leaf, score: 18.03 | N | N | N | N |
| vg0430344329 | C -> T | LOC_Os04g51200.1 | downstream_gene_variant ; 4393.0bp to feature; MODIFIER | silent_mutation | Average:13.082; most accessible tissue: Minghui63 young leaf, score: 18.03 | N | N | N | N |
| vg0430344329 | C -> T | LOC_Os04g51210.1 | intron_variant ; MODIFIER | silent_mutation | Average:13.082; most accessible tissue: Minghui63 young leaf, score: 18.03 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0430344329 | NA | 1.91E-06 | mr1040 | Jap_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 |
| vg0430344329 | NA | 1.87E-08 | mr1248 | Jap_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 |
| vg0430344329 | 3.98E-06 | 3.98E-06 | mr1254 | Jap_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 |
| vg0430344329 | NA | 9.18E-10 | mr1676_2 | Jap_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 |