| Variant ID: vg0912243494 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 12243494 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 318. )
AACAACACTGCCCCAATGCATATACAACATATTACTCATTAATCATATACTTAATCACTTTGTCTCATAGGTTATAATGGAGATTAATTAGATGAATAAA[T/C]
AGAAACGAGGAAGCAAGGACCAAACCATCAAACTGTAGCTACAGAGACCAAACTATACAATCACAAGATTCAAGAAAAAACAGAGAAACATGCAATTACC
GGTAATTGCATGTTTCTCTGTTTTTTCTTGAATCTTGTGATTGTATAGTTTGGTCTCTGTAGCTACAGTTTGATGGTTTGGTCCTTGCTTCCTCGTTTCT[A/G]
TTTATTCATCTAATTAATCTCCATTATAACCTATGAGACAAAGTGATTAAGTATATGATTAATGAGTAATATGTTGTATATGCATTGGGGCAGTGTTGTT
| 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 | 84.10% | 9.00% | 2.05% | 4.85% | NA |
| All Indica | 2759 | 91.10% | 0.30% | 0.69% | 7.94% | NA |
| All Japonica | 1512 | 68.50% | 26.90% | 4.50% | 0.20% | NA |
| Aus | 269 | 98.90% | 0.40% | 0.74% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.30% | 0.50% | 0.00% | NA |
| Indica II | 465 | 69.00% | 0.40% | 2.15% | 28.39% | NA |
| Indica III | 913 | 97.20% | 0.10% | 0.11% | 2.63% | NA |
| Indica Intermediate | 786 | 91.10% | 0.30% | 0.64% | 8.02% | NA |
| Temperate Japonica | 767 | 44.20% | 48.80% | 6.78% | 0.26% | NA |
| Tropical Japonica | 504 | 97.60% | 0.80% | 1.59% | 0.00% | NA |
| Japonica Intermediate | 241 | 84.60% | 11.60% | 3.32% | 0.41% | NA |
| VI/Aromatic | 96 | 93.80% | 3.10% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 8.90% | 5.56% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0912243494 | T -> DEL | N | N | silent_mutation | Average:52.27; most accessible tissue: Zhenshan97 root, score: 72.188 | N | N | N | N |
| vg0912243494 | T -> C | LOC_Os09g20380.1 | intron_variant ; MODIFIER | silent_mutation | Average:52.27; most accessible tissue: Zhenshan97 root, score: 72.188 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0912243494 | NA | 6.26E-07 | mr1011_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 |
| vg0912243494 | 1.06E-06 | 2.03E-08 | mr1321_2 | 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 |
| vg0912243494 | NA | 8.27E-06 | mr1321_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 |
| vg0912243494 | NA | 5.65E-07 | mr1449_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 |
| vg0912243494 | 3.10E-07 | NA | mr1768_2 | 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 |
| vg0912243494 | NA | 6.68E-07 | mr1768_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 |