| Variant ID: vg0417775732 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17775732 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGATATCCTTGAAATTGATCCAGAGAACATCTTCATCTTGTAAGAAGTCGGAGATCTTGATCCTCGCTCCGATAATCTCCCTACCGCTGGCGCTCATCTC[C/T]
ATGTACCGTTGATGGAATTTGTACATCTGTGTCGGTAGGGACTGCAGCTGCTCAGGCTTGACAAGCGGTTTACCGAGTTCGTACTGGTGTCTCACTTCCG
CGGAAGTGAGACACCAGTACGAACTCGGTAAACCGCTTGTCAAGCCTGAGCAGCTGCAGTCCCTACCGACACAGATGTACAAATTCCATCAACGGTACAT[G/A]
GAGATGAGCGCCAGCGGTAGGGAGATTATCGGAGCGAGGATCAAGATCTCCGACTTCTTACAAGATGAAGATGTTCTCTGGATCAATTTCAAGGATATCT
| 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 | 84.40% | 4.00% | 7.47% | 4.19% | NA |
| All Indica | 2759 | 97.00% | 0.30% | 2.32% | 0.36% | NA |
| All Japonica | 1512 | 57.10% | 11.60% | 18.85% | 12.43% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 88.60% | 1.20% | 9.92% | 0.34% | NA |
| Indica II | 465 | 98.50% | 0.00% | 0.00% | 1.51% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.00% | 0.30% | 0.64% | 0.13% | NA |
| Temperate Japonica | 767 | 41.50% | 12.10% | 22.95% | 23.47% | NA |
| Tropical Japonica | 504 | 75.00% | 11.10% | 13.29% | 0.60% | NA |
| Japonica Intermediate | 241 | 69.30% | 11.20% | 17.43% | 2.07% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0417775732 | C -> DEL | LOC_Os04g29820.1 | N | frameshift_variant | Average:25.354; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 | N | N | N | N |
| vg0417775732 | C -> T | LOC_Os04g29820.1 | missense_variant ; p.Met618Ile; MODERATE | nonsynonymous_codon ; M618I | Average:25.354; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 | unknown | unknown | DELETERIOUS | 0.02 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417775732 | NA | 7.62E-07 | mr1363_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 |
| vg0417775732 | 1.75E-06 | 3.23E-07 | mr1444_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 |
| vg0417775732 | NA | 7.14E-06 | mr1444_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 |