| Variant ID: vg1004623300 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4623300 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.20, others allele: 0.00, population size: 99. )
GCCTGTAAACTGCAAGACGAATTTATTAAGCCTAATTAATTCGTCGTTAGCAAATGTTTACTGTAGCATCACATTCTTAAATCATGGCGCAATTAGGCTT[G/A]
AAAGATTCATCTCGCAATTTACATGCAAATTGTACAATTGGTTTTTTTTGTCCACATTTAATGATCCATGCACATGTGTCCAAACATTTGATGTAACATT
AATGTTACATCAAATGTTTGGACACATGTGCATGGATCATTAAATGTGGACAAAAAAAACCAATTGTACAATTTGCATGTAAATTGCGAGATGAATCTTT[C/T]
AAGCCTAATTGCGCCATGATTTAAGAATGTGATGCTACAGTAAACATTTGCTAACGACGAATTAATTAGGCTTAATAAATTCGTCTTGCAGTTTACAGGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.80% | 28.40% | 9.10% | 30.74% | NA |
| All Indica | 2759 | 42.20% | 2.20% | 10.69% | 44.91% | NA |
| All Japonica | 1512 | 19.00% | 79.20% | 0.26% | 1.52% | NA |
| Aus | 269 | 4.50% | 1.50% | 38.29% | 55.76% | NA |
| Indica I | 595 | 41.00% | 1.30% | 3.53% | 54.12% | NA |
| Indica II | 465 | 37.80% | 2.20% | 5.38% | 54.62% | NA |
| Indica III | 913 | 49.70% | 1.40% | 20.92% | 27.93% | NA |
| Indica Intermediate | 786 | 36.80% | 3.90% | 7.38% | 51.91% | NA |
| Temperate Japonica | 767 | 6.30% | 93.10% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 32.90% | 65.10% | 0.00% | 1.98% | NA |
| Japonica Intermediate | 241 | 30.30% | 64.70% | 1.66% | 3.32% | NA |
| VI/Aromatic | 96 | 14.60% | 43.80% | 23.96% | 17.71% | NA |
| Intermediate | 90 | 28.90% | 38.90% | 5.56% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1004623300 | G -> A | LOC_Os10g08520.1 | upstream_gene_variant ; 2509.0bp to feature; MODIFIER | silent_mutation | Average:21.72; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1004623300 | G -> A | LOC_Os10g08530.1 | upstream_gene_variant ; 1932.0bp to feature; MODIFIER | silent_mutation | Average:21.72; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1004623300 | G -> A | LOC_Os10g08520-LOC_Os10g08530 | intergenic_region ; MODIFIER | silent_mutation | Average:21.72; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1004623300 | G -> DEL | N | N | silent_mutation | Average:21.72; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004623300 | NA | 6.02E-06 | mr1495 | 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 |
| vg1004623300 | NA | 1.47E-06 | mr1053_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 |
| vg1004623300 | 4.26E-06 | NA | mr1165_2 | 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 |
| vg1004623300 | NA | 4.25E-06 | mr1165_2 | 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 |