| Variant ID: vg0913440005 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 13440005 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTCGCTTCAATCTAGTCTTCATCTCCGATACTGATATTACCAAATTTGGTCGTTAACACATGCCCCCCAAGTCCGGAATATTCGATAATGTTTCGGATTT[G/A]
CCGCATATCGACTCCGAGCAAGTTTCGCACTCCGCCGTTTTCCGACCGTTATCCTCCGTGCTTTAAATACTAACCGCCACCCTGAAAAATCTTTACCCCG
CGGGGTAAAGATTTTTCAGGGTGGCGGTTAGTATTTAAAGCACGGAGGATAACGGTCGGAAAACGGCGGAGTGCGAAACTTGCTCGGAGTCGATATGCGG[C/T]
AAATCCGAAACATTATCGAATATTCCGGACTTGGGGGGCATGTGTTAACGACCAAATTTGGTAATATCAGTATCGGAGATGAAGACTAGATTGAAGCGAA
| 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 | 94.40% | 0.90% | 1.88% | 2.81% | NA |
| All Indica | 2759 | 97.80% | 0.00% | 0.43% | 1.78% | NA |
| All Japonica | 1512 | 92.30% | 2.90% | 4.76% | 0.00% | NA |
| Aus | 269 | 72.90% | 0.00% | 1.12% | 26.02% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.10% | 0.00% | 0.65% | 4.30% | NA |
| Indica III | 913 | 97.60% | 0.00% | 0.66% | 1.75% | NA |
| Indica Intermediate | 786 | 98.00% | 0.00% | 0.38% | 1.65% | NA |
| Temperate Japonica | 767 | 86.80% | 4.00% | 9.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.60% | 4.60% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 0.00% | 13.54% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0913440005 | G -> DEL | N | N | silent_mutation | Average:54.576; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg0913440005 | G -> A | LOC_Os09g22210.1 | upstream_gene_variant ; 4542.0bp to feature; MODIFIER | silent_mutation | Average:54.576; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg0913440005 | G -> A | LOC_Os09g22220.1 | upstream_gene_variant ; 217.0bp to feature; MODIFIER | silent_mutation | Average:54.576; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg0913440005 | G -> A | LOC_Os09g22230.1 | downstream_gene_variant ; 3934.0bp to feature; MODIFIER | silent_mutation | Average:54.576; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg0913440005 | G -> A | LOC_Os09g22210-LOC_Os09g22220 | intergenic_region ; MODIFIER | silent_mutation | Average:54.576; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0913440005 | NA | 6.79E-10 | Awn_length | Jap_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 |
| vg0913440005 | NA | 7.48E-06 | mr1677 | 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 |
| vg0913440005 | 1.05E-06 | 1.05E-06 | mr1986 | 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 |