| Variant ID: vg0614458476 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14458476 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 122. )
TTTTTCCCAAACCTAGAAGAGGAGTTCCTGGATGATGAAGGCTTTGGTGTCTAGCTCGTGCCTGCCGTCAAGCGCCTGTGGTCGTCGCCCTAGTCTTCCG[C/T]
TGTTTTTCTTTTGTCTTCATGTGTGCTGGGCCTTCACCGCCCATGTAATAAATTAACTATTTATGCTTCCGCTTGTTAAACTCTATATTGTATCAACTTT
AAAGTTGATACAATATAGAGTTTAACAAGCGGAAGCATAAATAGTTAATTTATTACATGGGCGGTGAAGGCCCAGCACACATGAAGACAAAAGAAAAACA[G/A]
CGGAAGACTAGGGCGACGACCACAGGCGCTTGACGGCAGGCACGAGCTAGACACCAAAGCCTTCATCATCCAGGAACTCCTCTTCTAGGTTTGGGAAAAA
| 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 | 62.30% | 21.60% | 12.34% | 3.81% | NA |
| All Indica | 2759 | 41.50% | 35.00% | 19.43% | 4.02% | NA |
| All Japonica | 1512 | 93.60% | 0.30% | 1.92% | 4.23% | NA |
| Aus | 269 | 85.50% | 11.20% | 2.23% | 1.12% | NA |
| Indica I | 595 | 39.80% | 16.80% | 38.15% | 5.21% | NA |
| Indica II | 465 | 31.60% | 47.50% | 16.56% | 4.30% | NA |
| Indica III | 913 | 43.60% | 41.50% | 11.72% | 3.18% | NA |
| Indica Intermediate | 786 | 46.30% | 33.80% | 15.90% | 3.94% | NA |
| Temperate Japonica | 767 | 97.50% | 0.10% | 1.30% | 1.04% | NA |
| Tropical Japonica | 504 | 87.50% | 0.60% | 3.37% | 8.53% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.00% | 0.83% | 5.39% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 65.60% | 22.20% | 11.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614458476 | C -> T | LOC_Os06g24630.1 | upstream_gene_variant ; 1931.0bp to feature; MODIFIER | silent_mutation | Average:17.343; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0614458476 | C -> T | LOC_Os06g24620.1 | intron_variant ; MODIFIER | silent_mutation | Average:17.343; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0614458476 | C -> DEL | N | N | silent_mutation | Average:17.343; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0614458476 | NA | 1.84E-06 | mr1042_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 |
| vg0614458476 | NA | 3.73E-07 | mr1167_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 |
| vg0614458476 | NA | 3.49E-06 | mr1608_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 |
| vg0614458476 | 9.77E-06 | 6.62E-08 | mr1950_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 |