| Variant ID: vg0136606599 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36606599 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 300. )
ATAAAATATGGTAAGAACTGCAAGTACTACATGCATGTCCATCTACCAAAAATACAACAATAACCATGATTTGACTTGATTACACCTTAATATATAAAAA[T/A]
TGACTCCAAAAGTTTCATCTCACTAATTTACATTATCCTAATCTGTTAAGCTGGTGGAACAGACCGCGCTAAGGTGTCACTGCTTTGCAAACCACTTTTC
GAAAAGTGGTTTGCAAAGCAGTGACACCTTAGCGCGGTCTGTTCCACCAGCTTAACAGATTAGGATAATGTAAATTAGTGAGATGAAACTTTTGGAGTCA[A/T]
TTTTTATATATTAAGGTGTAATCAAGTCAAATCATGGTTATTGTTGTATTTTTGGTAGATGGACATGCATGTAGTACTTGCAGTTCTTACCATATTTTAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.70% | 3.10% | 0.23% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 89.70% | 9.50% | 0.73% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 84.40% | 14.30% | 1.30% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.80% | 10.80% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136606599 | T -> A | LOC_Os01g63160.1 | 3_prime_UTR_variant ; 46.0bp to feature; MODIFIER | silent_mutation | Average:49.71; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0136606599 | T -> A | LOC_Os01g63170.1 | upstream_gene_variant ; 4178.0bp to feature; MODIFIER | silent_mutation | Average:49.71; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0136606599 | 6.90E-20 | 2.22E-26 | Awn_length | All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0136606599 | 1.52E-09 | 2.11E-14 | Awn_length | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |