| Variant ID: vg0909056772 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 9056772 |
| 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: 313. )
TTGCACATTCAACGACGACATCCACCAGAACAAATCATTGGTAATATAGGTGAGCGGACTACAAGGTCTAAGGTAACGACTCATGATGTTTGTGCAAATT[C/T]
TGCTTTTGTTGCTTCTTTTGAACCCAAAGATGTGTCACATGCATTAACTGATGAATCGTGGATTAACGCCATGCATGAAGAACTTGAAAATTTTGAGAGA
TCTCTCAAAATTTTCAAGTTCTTCATGCATGGCGTTAATCCACGATTCATCAGTTAATGCATGTGACACATCTTTGGGTTCAAAAGAAGCAACAAAAGCA[G/A]
AATTTGCACAAACATCATGAGTCGTTACCTTAGACCTTGTAGTCCGCTCACCTATATTACCAATGATTTGTTCTGGTGGATGTCGTCGTTGAATGTGCAA
| 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 | 87.80% | 11.90% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 92.70% | 7.20% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 79.40% | 20.60% | 0.07% | 0.00% | NA |
| Aus | 269 | 93.30% | 2.60% | 4.09% | 0.00% | NA |
| Indica I | 595 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 87.30% | 12.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.00% | 5.70% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 69.50% | 30.40% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 93.10% | 6.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 82.20% | 17.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 65.60% | 34.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 12.20% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0909056772 | C -> T | LOC_Os09g15020.1 | intron_variant ; MODIFIER | silent_mutation | Average:32.91; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0909056772 | NA | 1.13E-07 | 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 |
| vg0909056772 | 5.00E-06 | NA | mr1093 | 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 |