| Variant ID: vg0224382110 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 24382110 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCACCACCTTGTGGAGCTAGCCGGAAGACCCCTGGGCATTTCTCAAATGTGATTAGATAAAGGAGTCTGTACTGATAAAAACTATTTCTACAACAGATGG[C/T]
ATTTGGATTGTTAGTACACGAATTGGACTAGTGGACTTACTCAAATGATCCGTAAGTGTTAGGTTTGGATCTAAGTTGAATGGCCCTTCAACCACAAGAG
CTCTTGTGGTTGAAGGGCCATTCAACTTAGATCCAAACCTAACACTTACGGATCATTTGAGTAAGTCCACTAGTCCAATTCGTGTACTAACAATCCAAAT[G/A]
CCATCTGTTGTAGAAATAGTTTTTATCAGTACAGACTCCTTTATCTAATCACATTTGAGAAATGCCCAGGGGTCTTCCGGCTAGCTCCACAAGGTGGTGG
| 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 | 91.20% | 2.50% | 0.99% | 5.31% | NA |
| All Indica | 2759 | 92.90% | 0.90% | 0.87% | 5.33% | NA |
| All Japonica | 1512 | 86.70% | 5.80% | 1.46% | 6.08% | NA |
| Aus | 269 | 97.40% | 0.40% | 0.37% | 1.86% | NA |
| Indica I | 595 | 98.70% | 0.00% | 0.34% | 1.01% | NA |
| Indica II | 465 | 98.70% | 0.00% | 0.00% | 1.29% | NA |
| Indica III | 913 | 86.30% | 2.00% | 1.42% | 10.30% | NA |
| Indica Intermediate | 786 | 92.70% | 0.90% | 1.15% | 5.22% | NA |
| Temperate Japonica | 767 | 83.40% | 5.90% | 2.09% | 8.60% | NA |
| Tropical Japonica | 504 | 91.30% | 4.40% | 0.79% | 3.57% | NA |
| Japonica Intermediate | 241 | 87.60% | 8.30% | 0.83% | 3.32% | NA |
| VI/Aromatic | 96 | 92.70% | 3.10% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0224382110 | C -> T | LOC_Os02g40270.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.889; most accessible tissue: Minghui63 flower, score: 77.232 | N | N | N | N |
| vg0224382110 | C -> DEL | N | N | silent_mutation | Average:54.889; most accessible tissue: Minghui63 flower, score: 77.232 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0224382110 | 8.59E-06 | 8.59E-06 | mr1312_2 | Ind_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 |
| vg0224382110 | NA | 1.50E-06 | mr1528_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 |
| vg0224382110 | NA | 3.64E-06 | mr1682_2 | Ind_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 |
| vg0224382110 | 2.24E-06 | 2.24E-06 | mr1983_2 | Ind_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 |