| Variant ID: vg0719834473 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19834473 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAAACGAACCGGCGTGAATACGATAACAAAATTTTATCGGAATAAAAAACCCCTCAAACTGATAAATCCAATTCTCAAGTCTCAACAGCCAACAATTCAT[C/T]
ATAAAACAGTCTTAATAGTACATCACAAAACACAGTCTATGAAATAAATTATCTATGTTTAATAGAGTAATGTTGTTGATAAATCCTAATACAAGAAAAA
TTTTTCTTGTATTAGGATTTATCAACAACATTACTCTATTAAACATAGATAATTTATTTCATAGACTGTGTTTTGTGATGTACTATTAAGACTGTTTTAT[G/A]
ATGAATTGTTGGCTGTTGAGACTTGAGAATTGGATTTATCAGTTTGAGGGGTTTTTTATTCCGATAAAATTTTGTTATCGTATTCACGCCGGTTCGTTTT
| 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 | 39.10% | 7.70% | 0.30% | 52.92% | NA |
| All Indica | 2759 | 11.50% | 0.20% | 0.47% | 87.86% | NA |
| All Japonica | 1512 | 75.70% | 23.50% | 0.00% | 0.79% | NA |
| Aus | 269 | 88.80% | 0.00% | 0.00% | 11.15% | NA |
| Indica I | 595 | 5.00% | 0.00% | 0.84% | 94.12% | NA |
| Indica II | 465 | 7.10% | 0.00% | 0.00% | 92.90% | NA |
| Indica III | 913 | 17.40% | 0.00% | 0.00% | 82.58% | NA |
| Indica Intermediate | 786 | 12.10% | 0.60% | 1.02% | 86.26% | NA |
| Temperate Japonica | 767 | 55.50% | 43.20% | 0.00% | 1.30% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 90.00% | 9.10% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 56.70% | 3.30% | 1.11% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719834473 | C -> DEL | N | N | silent_mutation | Average:9.95; most accessible tissue: Callus, score: 52.841 | N | N | N | N |
| vg0719834473 | C -> T | LOC_Os07g33210.1 | upstream_gene_variant ; 4103.0bp to feature; MODIFIER | silent_mutation | Average:9.95; most accessible tissue: Callus, score: 52.841 | N | N | N | N |
| vg0719834473 | C -> T | LOC_Os07g33200.1 | downstream_gene_variant ; 1278.0bp to feature; MODIFIER | silent_mutation | Average:9.95; most accessible tissue: Callus, score: 52.841 | N | N | N | N |
| vg0719834473 | C -> T | LOC_Os07g33200-LOC_Os07g33210 | intergenic_region ; MODIFIER | silent_mutation | Average:9.95; most accessible tissue: Callus, score: 52.841 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0719834473 | 4.01E-07 | NA | Plant_height | 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 |
| vg0719834473 | 9.30E-06 | NA | Spikelet_length | All | Not | 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 |
| vg0719834473 | NA | 2.12E-06 | mr1993 | 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 |
| vg0719834473 | NA | 1.58E-06 | mr1761_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 |