| Variant ID: vg0910076716 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10076716 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGAAAAATTTCGGTCGAAATAATATCGTATCGGGGGTGACCGAAATGACCAAAATTTTCGAAATTTCAAAAATTTCAGTCCGAAATTTCCAACCCTGCTC[C/A]
GGTCCTTGGCCGGATCTGGACGACGGGATGGTTAAGGCGCTAGGGGCAGGGGATGAGGAAGGGAGACACAGATGGGAAAGGTGGAGGAGGCTCCAAAAGG
CCTTTTGGAGCCTCCTCCACCTTTCCCATCTGTGTCTCCCTTCCTCATCCCCTGCCCCTAGCGCCTTAACCATCCCGTCGTCCAGATCCGGCCAAGGACC[G/T]
GAGCAGGGTTGGAAATTTCGGACTGAAATTTTTGAAATTTCGAAAATTTTGGTCATTTCGGTCACCCCCGATACGATATTATTTCGACCGAAATTTTTCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.30% | 1.90% | 1.12% | 63.69% | NA |
| All Indica | 2759 | 6.00% | 0.00% | 0.69% | 93.29% | NA |
| All Japonica | 1512 | 82.30% | 5.90% | 1.92% | 9.85% | NA |
| Aus | 269 | 19.00% | 0.00% | 1.12% | 79.93% | NA |
| Indica I | 595 | 12.10% | 0.00% | 1.68% | 86.22% | NA |
| Indica II | 465 | 3.20% | 0.00% | 0.65% | 96.13% | NA |
| Indica III | 913 | 2.40% | 0.00% | 0.11% | 97.48% | NA |
| Indica Intermediate | 786 | 7.30% | 0.00% | 0.64% | 92.11% | NA |
| Temperate Japonica | 767 | 83.60% | 8.50% | 2.74% | 5.22% | NA |
| Tropical Japonica | 504 | 83.50% | 0.60% | 0.79% | 15.08% | NA |
| Japonica Intermediate | 241 | 75.90% | 8.70% | 1.66% | 13.69% | NA |
| VI/Aromatic | 96 | 64.60% | 0.00% | 0.00% | 35.42% | NA |
| Intermediate | 90 | 53.30% | 2.20% | 2.22% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910076716 | C -> DEL | N | N | silent_mutation | Average:11.769; most accessible tissue: Callus, score: 66.59 | N | N | N | N |
| vg0910076716 | C -> A | LOC_Os09g16458.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.769; most accessible tissue: Callus, score: 66.59 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0910076716 | 4.45E-06 | 4.45E-06 | mr1935 | 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 |
| vg0910076716 | NA | 5.12E-06 | mr1305_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 |