| Variant ID: vg0707304077 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 7304077 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACTGGTGTCTCCGCCTATACGGCTGGCCTATTATGCCGCCGTTCATAGGCGTTCACGTCTTCACAGACCGGCTTGCCTTCACCACTGCCGACTGGTGTTT[C/T]
CGCCTACACGGCTAGCCCATTATGTCGCCGCTGTTGGGCGCCTACGACTTCGCCGCCGGCCTGCCTCCGCAGCCGCCGACTGGTGTTTTCGCCTGCACGG
CCGTGCAGGCGAAAACACCAGTCGGCGGCTGCGGAGGCAGGCCGGCGGCGAAGTCGTAGGCGCCCAACAGCGGCGACATAATGGGCTAGCCGTGTAGGCG[G/A]
AAACACCAGTCGGCAGTGGTGAAGGCAAGCCGGTCTGTGAAGACGTGAACGCCTATGAACGGCGGCATAATAGGCCAGCCGTATAGGCGGAGACACCAGT
| 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 | 34.40% | 2.30% | 5.71% | 57.60% | NA |
| All Indica | 2759 | 9.00% | 0.10% | 6.67% | 84.27% | NA |
| All Japonica | 1512 | 76.50% | 2.20% | 4.37% | 16.93% | NA |
| Aus | 269 | 64.30% | 0.00% | 2.23% | 33.46% | NA |
| Indica I | 595 | 8.60% | 0.00% | 5.38% | 86.05% | NA |
| Indica II | 465 | 9.90% | 0.00% | 5.38% | 84.73% | NA |
| Indica III | 913 | 2.60% | 0.00% | 10.51% | 86.86% | NA |
| Indica Intermediate | 786 | 16.20% | 0.30% | 3.94% | 79.64% | NA |
| Temperate Japonica | 767 | 90.10% | 1.30% | 5.35% | 3.26% | NA |
| Tropical Japonica | 504 | 68.70% | 2.40% | 3.97% | 25.00% | NA |
| Japonica Intermediate | 241 | 49.40% | 5.00% | 2.07% | 43.57% | NA |
| VI/Aromatic | 96 | 9.40% | 68.80% | 9.38% | 12.50% | NA |
| Intermediate | 90 | 44.40% | 6.70% | 5.56% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0707304077 | C -> DEL | N | N | silent_mutation | Average:9.972; most accessible tissue: Callus, score: 33.391 | N | N | N | N |
| vg0707304077 | C -> T | LOC_Os07g12760-LOC_Os07g12770 | intergenic_region ; MODIFIER | silent_mutation | Average:9.972; most accessible tissue: Callus, score: 33.391 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0707304077 | 1.44E-08 | 4.01E-10 | mr1219 | 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 |
| vg0707304077 | 1.51E-06 | 3.14E-08 | mr1274 | 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 |
| vg0707304077 | NA | 5.00E-07 | mr1219_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 |
| vg0707304077 | 9.37E-07 | 2.46E-08 | mr1274_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 |