| Variant ID: vg0906091731 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 6091731 |
| 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: 254. )
TTTTCGTTGGTAGATTTTACAGCGGTGGTTCTTAGCGTCAATGATTAGTCGGTTGGTGTCTTAACGAGATGCATGACTTTTGAAAAAGATAGCTAGCGTT[C/T]
AGAGAGATGCACATATATATGTACACATATGTACTTCCCTAAATGTATAGTATAGTACAATATTAATTTCTTCCTCTATAAATACTACTGTATTTGTCTG
CAGACAAATACAGTAGTATTTATAGAGGAAGAAATTAATATTGTACTATACTATACATTTAGGGAAGTACATATGTGTACATATATATGTGCATCTCTCT[G/A]
AACGCTAGCTATCTTTTTCAAAAGTCATGCATCTCGTTAAGACACCAACCGACTAATCATTGACGCTAAGAACCACCGCTGTAAAATCTACCAACGAAAA
| 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 | 95.70% | 4.20% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 94.40% | 5.50% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 97.70% | 2.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 87.90% | 11.80% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.10% | 5.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0906091731 | C -> T | LOC_Os09g11005.1 | downstream_gene_variant ; 2175.0bp to feature; MODIFIER | silent_mutation | Average:60.851; most accessible tissue: Callus, score: 77.505 | N | N | N | N |
| vg0906091731 | C -> T | LOC_Os09g11000-LOC_Os09g11005 | intergenic_region ; MODIFIER | silent_mutation | Average:60.851; most accessible tissue: Callus, score: 77.505 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0906091731 | NA | 2.37E-09 | 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 |
| vg0906091731 | 5.53E-08 | 5.53E-08 | mr1389 | 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 |
| vg0906091731 | 1.69E-09 | 6.08E-14 | mr1038_2 | 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 |
| vg0906091731 | 4.16E-10 | 4.16E-10 | mr1389_2 | 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 |