| Variant ID: vg0712821619 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 12821619 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACCATGGGCTAGTTGGGTTGGCCCCAGGTTCGGCCGAACCTCCCTCATCGTCGCTGGATGCAGGGTTTCTTCTGGACGGTGTGGATTAGCTCCCAATGAC[G/A]
GTTGGAGGGTATTTCCGACCATTCCAACCGTCACAACCGTCATTGGGAGGCTATATAAACCCCTCACCTTCTTACTTCACTCATACACCTCAAGCAAGAG
CTCTTGCTTGAGGTGTATGAGTGAAGTAAGAAGGTGAGGGGTTTATATAGCCTCCCAATGACGGTTGTGACGGTTGGAATGGTCGGAAATACCCTCCAAC[C/T]
GTCATTGGGAGCTAATCCACACCGTCCAGAAGAAACCCTGCATCCAGCGACGATGAGGGAGGTTCGGCCGAACCTGGGGCCAACCCAACTAGCCCATGGT
| 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 | 89.20% | 8.50% | 1.82% | 0.44% | NA |
| All Indica | 2759 | 96.30% | 0.70% | 2.50% | 0.51% | NA |
| All Japonica | 1512 | 79.40% | 19.40% | 0.73% | 0.40% | NA |
| Aus | 269 | 93.30% | 4.50% | 2.23% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.00% | 1.01% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 97.20% | 0.10% | 1.86% | 0.88% | NA |
| Indica Intermediate | 786 | 91.30% | 2.20% | 5.73% | 0.76% | NA |
| Temperate Japonica | 767 | 67.00% | 32.90% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 96.20% | 0.60% | 1.98% | 1.19% | NA |
| Japonica Intermediate | 241 | 83.80% | 16.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 22.90% | 77.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 4.40% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0712821619 | G -> DEL | N | N | silent_mutation | Average:58.151; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |
| vg0712821619 | G -> A | LOC_Os07g22720.1 | upstream_gene_variant ; 2215.0bp to feature; MODIFIER | silent_mutation | Average:58.151; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |
| vg0712821619 | G -> A | LOC_Os07g22720.2 | upstream_gene_variant ; 2215.0bp to feature; MODIFIER | silent_mutation | Average:58.151; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |
| vg0712821619 | G -> A | LOC_Os07g22730.1 | downstream_gene_variant ; 4740.0bp to feature; MODIFIER | silent_mutation | Average:58.151; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |
| vg0712821619 | G -> A | LOC_Os07g22720-LOC_Os07g22730 | intergenic_region ; MODIFIER | silent_mutation | Average:58.151; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0712821619 | NA | 3.83E-17 | Awn_length | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0712821619 | 4.09E-07 | NA | mr1900 | 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 |
| vg0712821619 | NA | 1.56E-06 | mr1900 | 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 |