| Variant ID: vg0909866383 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 9866383 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 55. )
ATCATAGAGTAGCGGACAGAAAAGTTCGAATCAGATGAGCATCGTACCCTTTTCAAATCAACGGTGAGATGTCAGTGGTACCTCGAGGTACCTGGTACCT[G/A]
GTGGTACTTCCTCAAGGATGGTAAAAAATGCTCTTGGACAAAAGGGAATTTTGAAATAGTCAAGTGATTTGATCATGCTTATTTGAGTTTCATGTAATAC
GTATTACATGAAACTCAAATAAGCATGATCAAATCACTTGACTATTTCAAAATTCCCTTTTGTCCAAGAGCATTTTTTACCATCCTTGAGGAAGTACCAC[C/T]
AGGTACCAGGTACCTCGAGGTACCACTGACATCTCACCGTTGATTTGAAAAGGGTACGATGCTCATCTGATTCGAACTTTTCTGTCCGCTACTCTATGAT
| 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 | 38.20% | 22.50% | 1.38% | 37.98% | NA |
| All Indica | 2759 | 23.80% | 21.60% | 1.67% | 52.95% | NA |
| All Japonica | 1512 | 58.40% | 27.50% | 0.13% | 13.96% | NA |
| Aus | 269 | 75.10% | 1.50% | 2.97% | 20.45% | NA |
| Indica I | 595 | 9.90% | 16.00% | 2.69% | 71.43% | NA |
| Indica II | 465 | 15.30% | 19.80% | 1.72% | 63.23% | NA |
| Indica III | 913 | 39.30% | 26.00% | 0.66% | 34.06% | NA |
| Indica Intermediate | 786 | 21.20% | 21.90% | 2.04% | 54.83% | NA |
| Temperate Japonica | 767 | 80.20% | 2.30% | 0.13% | 17.34% | NA |
| Tropical Japonica | 504 | 16.50% | 71.20% | 0.00% | 12.30% | NA |
| Japonica Intermediate | 241 | 76.80% | 16.20% | 0.41% | 6.64% | NA |
| VI/Aromatic | 96 | 35.40% | 19.80% | 5.21% | 39.58% | NA |
| Intermediate | 90 | 33.30% | 28.90% | 4.44% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0909866383 | G -> DEL | N | N | silent_mutation | Average:24.296; most accessible tissue: Zhenshan97 young leaf, score: 50.669 | N | N | N | N |
| vg0909866383 | G -> A | LOC_Os09g16170.1 | upstream_gene_variant ; 3516.0bp to feature; MODIFIER | silent_mutation | Average:24.296; most accessible tissue: Zhenshan97 young leaf, score: 50.669 | N | N | N | N |
| vg0909866383 | G -> A | LOC_Os09g16180.1 | downstream_gene_variant ; 1146.0bp to feature; MODIFIER | silent_mutation | Average:24.296; most accessible tissue: Zhenshan97 young leaf, score: 50.669 | N | N | N | N |
| vg0909866383 | G -> A | LOC_Os09g16180-LOC_Os09g16190 | intergenic_region ; MODIFIER | silent_mutation | Average:24.296; most accessible tissue: Zhenshan97 young leaf, score: 50.669 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0909866383 | 5.40E-07 | 5.40E-07 | mr1260 | Ind_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 |
| vg0909866383 | NA | 8.19E-06 | mr1505 | Ind_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 |
| vg0909866383 | NA | 2.14E-07 | mr1807 | Ind_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 |