| Variant ID: vg0718406646 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 18406646 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATGCAAACCCAGGACGAAACCACCTGCCCCGTTGATGACATCACTCAGCGGACACCATGTGAGCTGCATATCCCCTTCAAGAACTTATCAATAAAGGTAA[A/G]
CTCGTAGTTTATAGATTTTAGATTTGGCCATTCCGCTAGTTGCTGCTTATATATGTTGATTACTAATAAATAACCTCTCACCACATGAAGGTGGCGTCGG
CCGACGCCACCTTCATGTGGTGAGAGGTTATTTATTAGTAATCAACATATATAAGCAGCAACTAGCGGAATGGCCAAATCTAAAATCTATAAACTACGAG[T/C]
TTACCTTTATTGATAAGTTCTTGAAGGGGATATGCAGCTCACATGGTGTCCGCTGAGTGATGTCATCAACGGGGCAGGTGGTTTCGTCCTGGGTTTGCAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.90% | 12.90% | 34.11% | 21.07% | NA |
| All Indica | 2759 | 26.40% | 1.80% | 47.26% | 24.50% | NA |
| All Japonica | 1512 | 42.10% | 35.00% | 10.12% | 12.76% | NA |
| Aus | 269 | 7.40% | 4.80% | 46.10% | 41.64% | NA |
| Indica I | 595 | 20.00% | 1.80% | 36.47% | 41.68% | NA |
| Indica II | 465 | 13.80% | 3.20% | 59.57% | 23.44% | NA |
| Indica III | 913 | 31.10% | 0.80% | 52.79% | 15.33% | NA |
| Indica Intermediate | 786 | 33.20% | 2.30% | 41.73% | 22.77% | NA |
| Temperate Japonica | 767 | 42.80% | 53.50% | 1.04% | 2.74% | NA |
| Tropical Japonica | 504 | 40.70% | 10.90% | 23.41% | 25.00% | NA |
| Japonica Intermediate | 241 | 43.20% | 26.60% | 11.20% | 19.09% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 3.12% | 5.21% | NA |
| Intermediate | 90 | 37.80% | 20.00% | 31.11% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0718406646 | A -> DEL | N | N | silent_mutation | Average:23.567; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0718406646 | A -> G | LOC_Os07g31100.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:23.567; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0718406646 | A -> G | LOC_Os07g31110.1 | upstream_gene_variant ; 1291.0bp to feature; MODIFIER | silent_mutation | Average:23.567; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0718406646 | A -> G | LOC_Os07g31080.1 | downstream_gene_variant ; 3258.0bp to feature; MODIFIER | silent_mutation | Average:23.567; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0718406646 | A -> G | LOC_Os07g31090.1 | downstream_gene_variant ; 1065.0bp to feature; MODIFIER | silent_mutation | Average:23.567; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0718406646 | NA | 4.01E-06 | mr1011_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 |
| vg0718406646 | NA | 4.55E-07 | mr1682_2 | Jap_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 |
| vg0718406646 | NA | 1.79E-06 | mr1754_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 |
| vg0718406646 | 5.43E-06 | 5.43E-06 | mr1754_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 |