| Variant ID: vg0318955179 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18955179 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCGTGCCGAGCCCGCCCCCGTTGTTCCTCAGGAGGATGGAGCCTCCGGCGTTGGCAGCACAGAGGATGCGTTGCTGCTCACCTTCCGCCCTGGCCCGTCG[T/C]
AGCAGTAGACGAGCAGTTAGTAGGCTTGCGCGTGTGTTCTTCTCGTTTGTTTTTCTGCTAGAGTCATATAGGGCATGGTTATGCCGGTGTGTGGTATAAC
GTTATACCACACACCGGCATAACCATGCCCTATATGACTCTAGCAGAAAAACAAACGAGAAGAACACACGCGCAAGCCTACTAACTGCTCGTCTACTGCT[A/G]
CGACGGGCCAGGGCGGAAGGTGAGCAGCAACGCATCCTCTGTGCTGCCAACGCCGGAGGCTCCATCCTCCTGAGGAACAACGGGGGCGGGCTCGGCACGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.50% | 0.90% | 24.61% | 37.03% | NA |
| All Indica | 2759 | 10.90% | 1.40% | 32.69% | 55.02% | NA |
| All Japonica | 1512 | 86.40% | 0.10% | 2.38% | 11.11% | NA |
| Aus | 269 | 13.80% | 1.50% | 68.40% | 16.36% | NA |
| Indica I | 595 | 7.90% | 0.20% | 16.13% | 75.80% | NA |
| Indica II | 465 | 6.90% | 1.30% | 27.53% | 64.30% | NA |
| Indica III | 913 | 13.30% | 2.30% | 48.52% | 35.93% | NA |
| Indica Intermediate | 786 | 12.80% | 1.30% | 29.90% | 55.98% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 66.90% | 0.20% | 2.58% | 30.36% | NA |
| Japonica Intermediate | 241 | 85.10% | 0.00% | 9.54% | 5.39% | NA |
| VI/Aromatic | 96 | 74.00% | 0.00% | 22.92% | 3.12% | NA |
| Intermediate | 90 | 60.00% | 0.00% | 21.11% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318955179 | T -> C | LOC_Os03g33130.1 | splice_donor_variant&intron_variant ; HIGH | splice_donor_variant | Average:11.997; most accessible tissue: Callus, score: 43.337 | N | N | N | N |
| vg0318955179 | T -> DEL | LOC_Os03g33130.1 | N | splice_donor_variant | Average:11.997; most accessible tissue: Callus, score: 43.337 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0318955179 | NA | 3.10E-06 | mr1215 | 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 |
| vg0318955179 | NA | 3.89E-12 | mr1386 | 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 |
| vg0318955179 | 7.93E-08 | 4.56E-14 | mr1750 | 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 |
| vg0318955179 | NA | 1.06E-12 | mr1751 | 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 |
| vg0318955179 | NA | 2.22E-06 | mr1751 | 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 |
| vg0318955179 | 2.99E-08 | 8.37E-19 | mr1750_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 |