| Variant ID: vg0907106741 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 7106741 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGTCATCATGGCCTCCCCTAAAATTAGAAATATTAATGGCATTAGTCGTTGTATAAGGTCATTCCCAACCCAAGACACTACACATAGTTTTCATAAATTT[C/T]
ACATCATTAAGAAACTAGTATTATACACTACTCTTCCAATGCAAACACCACTATTTCATACTTTAATTTAATGCTATTTATCTCACATGATGTCTTGGAT
ATCCAAGACATCATGTGAGATAAATAGCATTAAATTAAAGTATGAAATAGTGGTGTTTGCATTGGAAGAGTAGTGTATAATACTAGTTTCTTAATGATGT[G/A]
AAATTTATGAAAACTATGTGTAGTGTCTTGGGTTGGGAATGACCTTATACAACGACTAATGCCATTAATATTTCTAATTTTAGGGGAGGCCATGATGACT
| 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 | 86.60% | 2.10% | 1.61% | 9.71% | NA |
| All Indica | 2759 | 89.00% | 0.10% | 0.22% | 10.69% | NA |
| All Japonica | 1512 | 78.80% | 6.50% | 4.43% | 10.32% | NA |
| Aus | 269 | 98.90% | 0.00% | 0.00% | 1.12% | NA |
| Indica I | 595 | 98.70% | 0.00% | 0.34% | 1.01% | NA |
| Indica II | 465 | 97.00% | 0.00% | 0.00% | 3.01% | NA |
| Indica III | 913 | 72.90% | 0.00% | 0.44% | 26.62% | NA |
| Indica Intermediate | 786 | 95.70% | 0.30% | 0.00% | 4.07% | NA |
| Temperate Japonica | 767 | 79.70% | 12.00% | 6.78% | 1.56% | NA |
| Tropical Japonica | 504 | 86.10% | 0.00% | 0.60% | 13.29% | NA |
| Japonica Intermediate | 241 | 60.60% | 2.50% | 4.98% | 31.95% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 3.33% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0907106741 | C -> DEL | N | N | silent_mutation | Average:61.048; most accessible tissue: Zhenshan97 flower, score: 79.85 | N | N | N | N |
| vg0907106741 | C -> T | LOC_Os09g12420.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.048; most accessible tissue: Zhenshan97 flower, score: 79.85 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0907106741 | 8.24E-06 | NA | mr1238_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 |
| vg0907106741 | 2.37E-06 | NA | mr1841_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 |