| Variant ID: vg0203528644 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 3528644 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGTTCATCTTACACATAGAAAAATTGAAAAATTTAAATTATGATGCTCACGAATATTATCGGCCCCATCGTTTGGCTTATTCGTGGAATAAGCCAAACAT[C/T]
ATATTTGCAAACAAAAAATAATTTGTGAATAAAACTTTTATATACATGTTCTTAGCAACCTAAAAGTAAGAATTGAAAAATAAACTTCAATGAAAAAAAA
TTTTTTTTCATTGAAGTTTATTTTTCAATTCTTACTTTTAGGTTGCTAAGAACATGTATATAAAAGTTTTATTCACAAATTATTTTTTGTTTGCAAATAT[G/A]
ATGTTTGGCTTATTCCACGAATAAGCCAAACGATGGGGCCGATAATATTCGTGAGCATCATAATTTAAATTTTTCAATTTTTCTATGTGTAAGATGAACA
| 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 | 87.60% | 10.50% | 1.93% | 0.00% | NA |
| All Indica | 2759 | 96.40% | 2.40% | 1.20% | 0.00% | NA |
| All Japonica | 1512 | 74.30% | 22.30% | 3.44% | 0.00% | NA |
| Aus | 269 | 80.70% | 18.20% | 1.12% | 0.00% | NA |
| Indica I | 595 | 97.50% | 0.50% | 2.02% | 0.00% | NA |
| Indica II | 465 | 98.30% | 0.20% | 1.51% | 0.00% | NA |
| Indica III | 913 | 95.80% | 3.90% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 95.20% | 3.30% | 1.53% | 0.00% | NA |
| Temperate Japonica | 767 | 95.60% | 0.90% | 3.52% | 0.00% | NA |
| Tropical Japonica | 504 | 35.90% | 60.50% | 3.57% | 0.00% | NA |
| Japonica Intermediate | 241 | 86.70% | 10.40% | 2.90% | 0.00% | NA |
| VI/Aromatic | 96 | 75.00% | 25.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 21.10% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0203528644 | C -> T | LOC_Os02g06950.1 | intron_variant ; MODIFIER | silent_mutation | Average:33.312; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0203528644 | 6.17E-06 | NA | Grain_weight | All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0203528644 | NA | 4.83E-06 | mr1398_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 |
| vg0203528644 | NA | 4.74E-07 | mr1606_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 |
| vg0203528644 | NA | 2.52E-07 | mr1696_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 |