| Variant ID: vg1010574532 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 10574532 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TAAATGGACATTGATGCATGCATCCATGCACACAAGTATTTATAACCCACATGTAATATCTTGATTTGCTATTGGCTAGGAAATAGTGGGGATGGTGCAT[A/G]
TATGGAGTTTGTTGCTAAAGTAAATATAGTATAAGAGAGTTATTAGCTTTTCTTGGTCTTTGTGTACCTGTGAAATATTTAGATCAATTTGGAATGGAGG
CCTCCATTCCAAATTGATCTAAATATTTCACAGGTACACAAAGACCAAGAAAAGCTAATAACTCTCTTATACTATATTTACTTTAGCAACAAACTCCATA[T/C]
ATGCACCATCCCCACTATTTCCTAGCCAATAGCAAATCAAGATATTACATGTGGGTTATAAATACTTGTGTGCATGGATGCATGCATCAATGTCCATTTA
| 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 | 65.70% | 7.20% | 0.74% | 26.30% | NA |
| All Indica | 2759 | 79.30% | 0.10% | 0.76% | 19.86% | NA |
| All Japonica | 1512 | 56.50% | 20.50% | 0.73% | 22.22% | NA |
| Aus | 269 | 2.20% | 0.70% | 1.12% | 95.91% | NA |
| Indica I | 595 | 96.50% | 0.20% | 0.17% | 3.19% | NA |
| Indica II | 465 | 89.50% | 0.00% | 0.65% | 9.89% | NA |
| Indica III | 913 | 66.30% | 0.00% | 1.10% | 32.64% | NA |
| Indica Intermediate | 786 | 75.40% | 0.10% | 0.89% | 23.54% | NA |
| Temperate Japonica | 767 | 67.90% | 27.20% | 0.65% | 4.17% | NA |
| Tropical Japonica | 504 | 48.20% | 3.80% | 0.60% | 47.42% | NA |
| Japonica Intermediate | 241 | 37.80% | 34.00% | 1.24% | 26.97% | NA |
| VI/Aromatic | 96 | 4.20% | 16.70% | 0.00% | 79.17% | NA |
| Intermediate | 90 | 58.90% | 13.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1010574532 | A -> G | LOC_Os10g20860.1 | upstream_gene_variant ; 543.0bp to feature; MODIFIER | silent_mutation | Average:33.927; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |
| vg1010574532 | A -> G | LOC_Os10g20870.1 | downstream_gene_variant ; 468.0bp to feature; MODIFIER | silent_mutation | Average:33.927; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |
| vg1010574532 | A -> G | LOC_Os10g20880.1 | downstream_gene_variant ; 3278.0bp to feature; MODIFIER | silent_mutation | Average:33.927; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |
| vg1010574532 | A -> G | LOC_Os10g20860-LOC_Os10g20870 | intergenic_region ; MODIFIER | silent_mutation | Average:33.927; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |
| vg1010574532 | A -> DEL | N | N | silent_mutation | Average:33.927; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1010574532 | NA | 5.93E-07 | mr1210 | 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 |
| vg1010574532 | 4.59E-06 | NA | mr1305 | 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 |
| vg1010574532 | NA | 5.05E-07 | mr1305 | 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 |
| vg1010574532 | 8.52E-06 | 3.25E-09 | mr1585 | 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 |
| vg1010574532 | 4.31E-06 | NA | mr1586 | 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 |
| vg1010574532 | NA | 5.32E-07 | mr1586 | 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 |
| vg1010574532 | NA | 1.45E-06 | mr1305_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 |
| vg1010574532 | 4.66E-06 | NA | mr1585_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 |
| vg1010574532 | 6.76E-07 | 1.95E-08 | mr1585_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 |
| vg1010574532 | 4.55E-06 | 4.55E-06 | mr1648_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 |
| vg1010574532 | NA | 3.56E-06 | mr1703_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 |
| vg1010574532 | NA | 2.20E-06 | mr1765_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 |