| Variant ID: vg1021218403 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 21218403 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 94. )
TGGAGGTACCAAGGTTAAAGGGGAGAGACCGCCCTCAGCATCCATGTGGCACCTTCCCCCTAGGAGGTCGGGCCGTGGATGGGTGGCAGCTGCCCCTTTC[G/A]
AACCCGAGGGGTCGGACTGCCCCCGACCCCTCCTGGTGGTCACGGCGTGGCCGCCATGCAAGTGAGGCTTGGTGGATGCTCCTCAGCGCTCACCTAACCG
CGGTTAGGTGAGCGCTGAGGAGCATCCACCAAGCCTCACTTGCATGGCGGCCACGCCGTGACCACCAGGAGGGGTCGGGGGCAGTCCGACCCCTCGGGTT[C/T]
GAAAGGGGCAGCTGCCACCCATCCACGGCCCGACCTCCTAGGGGGAAGGTGCCACATGGATGCTGAGGGCGGTCTCTCCCCTTTAACCTTGGTACCTCCA
| 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 | 36.40% | 6.50% | 1.48% | 55.61% | NA |
| All Indica | 2759 | 3.30% | 2.00% | 1.56% | 93.15% | NA |
| All Japonica | 1512 | 98.60% | 0.30% | 0.00% | 1.12% | NA |
| Aus | 269 | 0.70% | 87.00% | 9.29% | 2.97% | NA |
| Indica I | 595 | 5.40% | 0.20% | 1.68% | 92.77% | NA |
| Indica II | 465 | 1.70% | 1.70% | 1.94% | 94.62% | NA |
| Indica III | 913 | 1.90% | 1.90% | 1.10% | 95.18% | NA |
| Indica Intermediate | 786 | 4.30% | 3.70% | 1.78% | 90.20% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.00% | 1.56% | NA |
| Tropical Japonica | 504 | 98.80% | 0.80% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 90.60% | 8.30% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 55.60% | 6.70% | 1.11% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1021218403 | G -> A | LOC_Os10g39700.1 | upstream_gene_variant ; 1082.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1021218403 | G -> A | LOC_Os10g39690-LOC_Os10g39700 | intergenic_region ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1021218403 | G -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1021218403 | NA | 3.69E-06 | mr1230 | 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 |
| vg1021218403 | NA | 4.43E-07 | mr1662 | 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 |
| vg1021218403 | NA | 2.79E-20 | mr1305_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 |
| vg1021218403 | 7.90E-07 | NA | mr1383_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 |
| vg1021218403 | NA | 2.65E-07 | mr1522_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 |
| vg1021218403 | NA | 5.60E-20 | mr1817_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 |