| Variant ID: vg1207388082 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 7388082 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTGGCTTTGTGGACATGGTCCATTCTACGAGCGTGTGGTGGGCTGGGAAAAATAGAAGCCCGTCCATGCGCTGGGAGCACGCTTGGCTGGGCTTGTCCGT[G/A]
CGTACGGGACAGCCAACGGTGGTTCGACAGTGTCTCCCATAATTCCCCGTAACGGTCTGTGAGCAGCTGTGCTTCACTGTGTCTTCATCAATGCCACCCA
TGGGTGGCATTGATGAAGACACAGTGAAGCACAGCTGCTCACAGACCGTTACGGGGAATTATGGGAGACACTGTCGAACCACCGTTGGCTGTCCCGTACG[C/T]
ACGGACAAGCCCAGCCAAGCGTGCTCCCAGCGCATGGACGGGCTTCTATTTTTCCCAGCCCACCACACGCTCGTAGAATGGACCATGTCCACAAAGCCAA
| 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 | 79.40% | 7.60% | 7.98% | 4.99% | NA |
| All Indica | 2759 | 85.70% | 0.40% | 8.08% | 5.80% | NA |
| All Japonica | 1512 | 65.90% | 22.60% | 8.13% | 3.31% | NA |
| Aus | 269 | 95.90% | 0.00% | 2.23% | 1.86% | NA |
| Indica I | 595 | 88.20% | 0.70% | 4.71% | 6.39% | NA |
| Indica II | 465 | 87.50% | 0.40% | 6.02% | 6.02% | NA |
| Indica III | 913 | 83.00% | 0.40% | 10.51% | 6.02% | NA |
| Indica Intermediate | 786 | 85.80% | 0.30% | 9.03% | 4.96% | NA |
| Temperate Japonica | 767 | 74.80% | 10.40% | 11.21% | 3.52% | NA |
| Tropical Japonica | 504 | 55.40% | 36.30% | 4.37% | 3.97% | NA |
| Japonica Intermediate | 241 | 59.80% | 32.80% | 6.22% | 1.24% | NA |
| VI/Aromatic | 96 | 61.50% | 0.00% | 18.75% | 19.79% | NA |
| Intermediate | 90 | 83.30% | 6.70% | 7.78% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1207388082 | G -> DEL | N | N | silent_mutation | Average:11.367; most accessible tissue: Zhenshan97 flower, score: 16.6 | N | N | N | N |
| vg1207388082 | G -> A | LOC_Os12g13280.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:11.367; most accessible tissue: Zhenshan97 flower, score: 16.6 | N | N | N | N |
| vg1207388082 | G -> A | LOC_Os12g13270.1 | upstream_gene_variant ; 3488.0bp to feature; MODIFIER | silent_mutation | Average:11.367; most accessible tissue: Zhenshan97 flower, score: 16.6 | N | N | N | N |
| vg1207388082 | G -> A | LOC_Os12g13290.1 | upstream_gene_variant ; 1557.0bp to feature; MODIFIER | silent_mutation | Average:11.367; most accessible tissue: Zhenshan97 flower, score: 16.6 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1207388082 | 2.86E-06 | NA | mr1115_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 |
| vg1207388082 | NA | 1.72E-06 | mr1149_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 |
| vg1207388082 | NA | 2.43E-06 | mr1441_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 |