| Variant ID: vg1010575676 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 10575676 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCACCTACCACCATGGCCTTCACTTCTGCCCTCGAGCTCCGGTCATTTCCACTTCCATCAATGATCGTCCGCCACTAAGGCCTAGACCTCTTCCCCCAAG[A/C]
TCAGGTGACCGTCGCCTCCATCCACAAGTGCCAACCCCCTCTGCCTCTGCCTCCACCCCCACATCCATCCACAAGCACCCACCACCGTGCCCTCACTACA
TGTAGTGAGGGCACGGTGGTGGGTGCTTGTGGATGGATGTGGGGGTGGAGGCAGAGGCAGAGGGGGTTGGCACTTGTGGATGGAGGCGACGGTCACCTGA[T/G]
CTTGGGGGAAGAGGTCTAGGCCTTAGTGGCGGACGATCATTGATGGAAGTGGAAATGACCGGAGCTCGAGGGCAGAAGTGAAGGCCATGGTGGTAGGTGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.30% | 20.30% | 0.40% | 26.94% | NA |
| All Indica | 2759 | 78.10% | 0.90% | 0.47% | 20.51% | NA |
| All Japonica | 1512 | 16.90% | 60.10% | 0.20% | 22.82% | NA |
| Aus | 269 | 1.90% | 0.00% | 0.74% | 97.40% | NA |
| Indica I | 595 | 96.30% | 0.20% | 0.00% | 3.53% | NA |
| Indica II | 465 | 88.40% | 0.90% | 0.22% | 10.54% | NA |
| Indica III | 913 | 64.30% | 1.50% | 0.66% | 33.52% | NA |
| Indica Intermediate | 786 | 74.20% | 0.90% | 0.76% | 24.17% | NA |
| Temperate Japonica | 767 | 19.00% | 76.40% | 0.26% | 4.30% | NA |
| Tropical Japonica | 504 | 4.40% | 47.20% | 0.20% | 48.21% | NA |
| Japonica Intermediate | 241 | 36.10% | 35.30% | 0.00% | 28.63% | NA |
| VI/Aromatic | 96 | 20.80% | 0.00% | 1.04% | 78.12% | NA |
| Intermediate | 90 | 43.30% | 28.90% | 0.00% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1010575676 | A -> C | LOC_Os10g20860.1 | upstream_gene_variant ; 1687.0bp to feature; MODIFIER | silent_mutation | Average:52.556; most accessible tissue: Minghui63 young leaf, score: 75.937 | N | N | N | N |
| vg1010575676 | A -> C | LOC_Os10g20870.1 | upstream_gene_variant ; 136.0bp to feature; MODIFIER | silent_mutation | Average:52.556; most accessible tissue: Minghui63 young leaf, score: 75.937 | N | N | N | N |
| vg1010575676 | A -> C | LOC_Os10g20880.1 | downstream_gene_variant ; 2134.0bp to feature; MODIFIER | silent_mutation | Average:52.556; most accessible tissue: Minghui63 young leaf, score: 75.937 | N | N | N | N |
| vg1010575676 | A -> C | LOC_Os10g20870-LOC_Os10g20880 | intergenic_region ; MODIFIER | silent_mutation | Average:52.556; most accessible tissue: Minghui63 young leaf, score: 75.937 | N | N | N | N |
| vg1010575676 | A -> DEL | N | N | silent_mutation | Average:52.556; most accessible tissue: Minghui63 young leaf, score: 75.937 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1010575676 | 1.04E-08 | 5.20E-09 | mr1517 | 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 |
| vg1010575676 | 4.68E-06 | NA | mr1536 | 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 |
| vg1010575676 | 1.25E-06 | NA | mr1718 | 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 |