| Variant ID: vg1001967604 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1967604 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCGACTGCTTCTCACTTGAATATATCAAGGATAAAAAATATGAAAAGGGCCGAATGATAAACACTCAAAAGGTCCAAAAACAGATATATTTGGTAGGAAT[C/T]
CGAGTAAGAAACTCTTAAAATGATCCACCAAATATGATAAAGATCATGGTAATTAAGAAGTTCATTAGCCTAGGCTATAACCCTTACCATAATCAAAATA
TATTTTGATTATGGTAAGGGTTATAGCCTAGGCTAATGAACTTCTTAATTACCATGATCTTTATCATATTTGGTGGATCATTTTAAGAGTTTCTTACTCG[G/A]
ATTCCTACCAAATATATCTGTTTTTGGACCTTTTGAGTGTTTATCATTCGGCCCTTTTCATATTTTTTATCCTTGATATATTCAAGTGAGAAGCAGTCGG
| 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 | 91.80% | 7.80% | 0.32% | 0.08% | NA |
| All Indica | 2759 | 99.50% | 0.30% | 0.14% | 0.14% | NA |
| All Japonica | 1512 | 76.10% | 23.30% | 0.60% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.40% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.30% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.90% | 0.40% | 0.22% | 0.44% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 90.90% | 8.60% | 0.52% | 0.00% | NA |
| Tropical Japonica | 504 | 54.20% | 45.20% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 75.10% | 24.10% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 8.90% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001967604 | C -> T | LOC_Os10g04220.1 | upstream_gene_variant ; 709.0bp to feature; MODIFIER | silent_mutation | Average:18.205; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1001967604 | C -> T | LOC_Os10g04210.1 | downstream_gene_variant ; 3714.0bp to feature; MODIFIER | silent_mutation | Average:18.205; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1001967604 | C -> T | LOC_Os10g04230.1 | downstream_gene_variant ; 3501.0bp to feature; MODIFIER | silent_mutation | Average:18.205; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1001967604 | C -> T | LOC_Os10g04210-LOC_Os10g04220 | intergenic_region ; MODIFIER | silent_mutation | Average:18.205; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1001967604 | C -> DEL | N | N | silent_mutation | Average:18.205; 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 |
|---|---|---|---|---|---|---|
| vg1001967604 | 1.81E-06 | NA | mr1825 | 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 |
| vg1001967604 | 5.31E-06 | NA | mr1825 | 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 |
| vg1001967604 | 3.59E-06 | NA | mr1310_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 |