| Variant ID: vg0417379902 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17379902 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCACTATTCGTGTTTCGCTTTGGGGAGACCGCGCTACTGAGTTTCCTGCAGAAGAGTCTTCTCTAGGGGTCAGTCAGAACAACAAATTGTGATATTTGT[T/C]
GGCACGTTGGTGAAAGGATTCAAAAGTAAGCATGTCATGATGATTTTTCTTAGGAAGTTTCTGTGCATCTTACTACATGCTCATCCTATAGCGCCATGCA
TGCATGGCGCTATAGGATGAGCATGTAGTAAGATGCACAGAAACTTCCTAAGAAAAATCATCATGACATGCTTACTTTTGAATCCTTTCACCAACGTGCC[A/G]
ACAAATATCACAATTTGTTGTTCTGACTGACCCCTAGAGAAGACTCTTCTGCAGGAAACTCAGTAGCGCGGTCTCCCCAAAGCGAAACACGAATAGTGGC
| 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 | 66.90% | 16.10% | 8.25% | 8.74% | NA |
| All Indica | 2759 | 83.20% | 6.00% | 5.51% | 5.29% | NA |
| All Japonica | 1512 | 34.40% | 36.60% | 12.63% | 16.40% | NA |
| Aus | 269 | 92.60% | 1.50% | 3.35% | 2.60% | NA |
| Indica I | 595 | 61.30% | 10.90% | 13.11% | 14.62% | NA |
| Indica II | 465 | 86.00% | 8.20% | 4.73% | 1.08% | NA |
| Indica III | 913 | 92.00% | 2.10% | 1.97% | 3.94% | NA |
| Indica Intermediate | 786 | 87.80% | 5.60% | 4.33% | 2.29% | NA |
| Temperate Japonica | 767 | 31.00% | 21.30% | 19.69% | 28.03% | NA |
| Tropical Japonica | 504 | 41.50% | 55.40% | 2.98% | 0.20% | NA |
| Japonica Intermediate | 241 | 30.30% | 46.10% | 10.37% | 13.28% | NA |
| VI/Aromatic | 96 | 49.00% | 14.60% | 28.12% | 8.33% | NA |
| Intermediate | 90 | 58.90% | 24.40% | 12.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0417379902 | T -> C | LOC_Os04g29310.1 | intron_variant ; MODIFIER | silent_mutation | Average:29.823; most accessible tissue: Zhenshan97 young leaf, score: 39.843 | N | N | N | N |
| vg0417379902 | T -> DEL | N | N | silent_mutation | Average:29.823; most accessible tissue: Zhenshan97 young leaf, score: 39.843 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417379902 | NA | 4.40E-06 | mr1024_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 |
| vg0417379902 | NA | 7.10E-06 | mr1204_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 |
| vg0417379902 | 6.03E-06 | NA | mr1480_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 |
| vg0417379902 | 1.65E-06 | NA | mr1968_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 |