| Variant ID: vg0715512638 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 15512638 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTAGCATTGTATTGTTGTCAAGTGATAATTGACACCTGAAATATGATGTGAAATTATTTAAAATAGGAAAAAGTGCTAATTACCCCATAAACCCAAAAA[C/A]
CAGACATTTTTCACCCTCAATTATTAATACCGGACGAATTACCCCTAACTCAACCCGGAGTGGTTTTATTCCGAAGTGACAGTCTAGTTAACACTTTTTA
TAAAAAGTGTTAACTAGACTGTCACTTCGGAATAAAACCACTCCGGGTTGAGTTAGGGGTAATTCGTCCGGTATTAATAATTGAGGGTGAAAAATGTCTG[G/T]
TTTTTGGGTTTATGGGGTAATTAGCACTTTTTCCTATTTTAAATAATTTCACATCATATTTCAGGTGTCAATTATCACTTGACAACAATACAATGCTAAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.70% | 25.10% | 4.17% | 0.00% | NA |
| All Indica | 2759 | 93.00% | 3.10% | 3.88% | 0.00% | NA |
| All Japonica | 1512 | 30.60% | 64.00% | 5.42% | 0.00% | NA |
| Aus | 269 | 88.50% | 9.30% | 2.23% | 0.00% | NA |
| Indica I | 595 | 89.60% | 1.20% | 9.24% | 0.00% | NA |
| Indica II | 465 | 94.60% | 1.50% | 3.87% | 0.00% | NA |
| Indica III | 913 | 98.90% | 0.90% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 87.80% | 8.10% | 4.07% | 0.00% | NA |
| Temperate Japonica | 767 | 52.00% | 39.90% | 8.08% | 0.00% | NA |
| Tropical Japonica | 504 | 2.40% | 95.60% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 21.60% | 74.30% | 4.15% | 0.00% | NA |
| VI/Aromatic | 96 | 12.50% | 87.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 27.80% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0715512638 | C -> A | LOC_Os07g26820.1 | upstream_gene_variant ; 4090.0bp to feature; MODIFIER | silent_mutation | Average:49.188; most accessible tissue: Zhenshan97 young leaf, score: 62.534 | N | N | N | N |
| vg0715512638 | C -> A | LOC_Os07g26810-LOC_Os07g26820 | intergenic_region ; MODIFIER | silent_mutation | Average:49.188; most accessible tissue: Zhenshan97 young leaf, score: 62.534 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0715512638 | NA | 5.62E-07 | mr1915 | 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 |
| vg0715512638 | NA | 3.80E-09 | mr1379_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 |
| vg0715512638 | 2.55E-06 | 2.55E-06 | mr1406_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 |