| Variant ID: vg0414573200 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 14573200 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, C: 0.38, others allele: 0.00, population size: 78. )
GCACCCGGCCAACAGCTTTTCAACGGCCACCCGGGCCAACAACTTTTCAAACGGCCACCCGGGCCTAGCTGATCCCATCAGCTACAGATTTTTCAAACAT[T/C]
GAACCCCTTTTCTCAACAGCAATTTCACAAGCAGTAGTCAAACAAAACTACGCTAGGAATCACCACACATCCGCCCATGACCGTGGGCACGGCTGTTCGA
TCGAACAGCCGTGCCCACGGTCATGGGCGGATGTGTGGTGATTCCTAGCGTAGTTTTGTTTGACTACTGCTTGTGAAATTGCTGTTGAGAAAAGGGGTTC[A/G]
ATGTTTGAAAAATCTGTAGCTGATGGGATCAGCTAGGCCCGGGTGGCCGTTTGAAAAGTTGTTGGCCCGGGTGGCCGTTGAAAAGCTGTTGGCCGGGTGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.20% | 1.10% | 22.53% | 13.16% | NA |
| All Indica | 2759 | 55.00% | 1.80% | 25.59% | 17.62% | NA |
| All Japonica | 1512 | 87.70% | 0.10% | 5.42% | 6.81% | NA |
| Aus | 269 | 6.30% | 0.70% | 86.62% | 6.32% | NA |
| Indica I | 595 | 43.90% | 1.20% | 29.75% | 25.21% | NA |
| Indica II | 465 | 24.10% | 3.20% | 41.72% | 30.97% | NA |
| Indica III | 913 | 80.20% | 0.70% | 15.66% | 3.50% | NA |
| Indica Intermediate | 786 | 52.40% | 2.80% | 24.43% | 20.36% | NA |
| Temperate Japonica | 767 | 85.30% | 0.00% | 6.39% | 8.34% | NA |
| Tropical Japonica | 504 | 92.10% | 0.20% | 2.78% | 4.96% | NA |
| Japonica Intermediate | 241 | 86.30% | 0.00% | 7.88% | 5.81% | NA |
| VI/Aromatic | 96 | 62.50% | 0.00% | 26.04% | 11.46% | NA |
| Intermediate | 90 | 73.30% | 0.00% | 21.11% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0414573200 | T -> C | LOC_Os04g25210.1 | downstream_gene_variant ; 3316.0bp to feature; MODIFIER | silent_mutation | Average:13.59; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0414573200 | T -> C | LOC_Os04g25190-LOC_Os04g25210 | intergenic_region ; MODIFIER | silent_mutation | Average:13.59; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0414573200 | T -> DEL | N | N | silent_mutation | Average:13.59; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0414573200 | NA | 5.03E-06 | mr1192 | 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 |
| vg0414573200 | NA | 4.44E-06 | mr1291 | 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 |
| vg0414573200 | 1.93E-06 | 1.93E-06 | mr1473 | 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 |
| vg0414573200 | NA | 9.56E-10 | mr1722 | 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 |
| vg0414573200 | 1.86E-06 | 1.86E-06 | mr1848 | 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 |