| Variant ID: vg0909184912 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 9184912 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCGGGGGCTCGTCGCTGGGTATTACATTGTCGGTTGTCGGCTGATTGTCACTTGGGTGATCTTCTGTGGTTGGCTCGGTCTCTTTTGAAGGACCCGTCTC[T/C]
ATGTCAATTGGTTTAGAATCTTTTCCAGAAGGATCTATGTCAGATGGCTTCCTACAAGTTTGAGTTACGCCATTATTATTATTTCAATAGTGGGTGAGCA
TGCTCACCCACTATTGAAATAATAATAATGGCGTAACTCAAACTTGTAGGAAGCCATCTGACATAGATCCTTCTGGAAAAGATTCTAAACCAATTGACAT[A/G]
GAGACGGGTCCTTCAAAAGAGACCGAGCCAACCACAGAAGATCACCCAAGTGACAATCAGCCGACAACCGACAATGTAATACCCAGCGACGAGCCCCCGA
| 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 | 30.40% | 0.70% | 9.50% | 59.37% | NA |
| All Indica | 2759 | 7.10% | 0.60% | 7.83% | 84.52% | NA |
| All Japonica | 1512 | 77.30% | 0.10% | 5.16% | 17.46% | NA |
| Aus | 269 | 4.50% | 0.40% | 31.97% | 63.20% | NA |
| Indica I | 595 | 8.60% | 0.20% | 4.71% | 86.55% | NA |
| Indica II | 465 | 3.40% | 0.90% | 10.11% | 85.59% | NA |
| Indica III | 913 | 7.80% | 0.70% | 9.09% | 82.48% | NA |
| Indica Intermediate | 786 | 7.30% | 0.60% | 7.38% | 84.73% | NA |
| Temperate Japonica | 767 | 75.50% | 0.00% | 8.21% | 16.30% | NA |
| Tropical Japonica | 504 | 84.50% | 0.00% | 1.98% | 13.49% | NA |
| Japonica Intermediate | 241 | 68.00% | 0.40% | 2.07% | 29.46% | NA |
| VI/Aromatic | 96 | 16.70% | 14.60% | 56.25% | 12.50% | NA |
| Intermediate | 90 | 51.10% | 1.10% | 16.67% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0909184912 | T -> DEL | LOC_Os09g15140.1 | N | frameshift_variant | Average:10.479; most accessible tissue: Callus, score: 43.21 | N | N | N | N |
| vg0909184912 | T -> C | LOC_Os09g15140.1 | missense_variant ; p.Ile376Met; MODERATE | nonsynonymous_codon ; I376M | Average:10.479; most accessible tissue: Callus, score: 43.21 | unknown | unknown | TOLERATED | 0.83 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0909184912 | 1.60E-06 | 1.60E-06 | mr1360_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 |
| vg0909184912 | 8.98E-06 | 8.98E-06 | mr1647_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 |
| vg0909184912 | 4.93E-06 | 4.93E-06 | mr1657_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 |