| Variant ID: vg0907797330 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 7797330 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 103. )
TAATGCATAACACTCCGGTGTGAGTTAGCTGTGTCTATGGCTAACGAATGTCAGGGCGTTACTGCTCCTCTCTCTCCCCTCAGCGCCCCTCTCGATAACC[G/A]
ATGTGATGGTTCCCAACCATCGTGTCCCTGCGGTTGCCACCGCTTCACATTTATATGTACTCTTGATCAATGAGAAACTATCAATTCGCTCTATTATGTC
GACATAATAGAGCGAATTGATAGTTTCTCATTGATCAAGAGTACATATAAATGTGAAGCGGTGGCAACCGCAGGGACACGATGGTTGGGAACCATCACAT[C/T]
GGTTATCGAGAGGGGCGCTGAGGGGAGAGAGAGGAGCAGTAACGCCCTGACATTCGTTAGCCATAGACACAGCTAACTCACACCGGAGTGTTATGCATTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.30% | 16.30% | 0.04% | 0.34% | NA |
| All Indica | 2759 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 57.00% | 41.80% | 0.13% | 1.06% | NA |
| Aus | 269 | 75.10% | 24.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.70% | 2.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 23.20% | 76.50% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 96.40% | 0.60% | 0.00% | 2.98% | NA |
| Japonica Intermediate | 241 | 82.20% | 17.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 17.80% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0907797330 | G -> DEL | N | N | silent_mutation | Average:70.445; most accessible tissue: Minghui63 panicle, score: 82.128 | N | N | N | N |
| vg0907797330 | G -> A | LOC_Os09g13470.1 | upstream_gene_variant ; 538.0bp to feature; MODIFIER | silent_mutation | Average:70.445; most accessible tissue: Minghui63 panicle, score: 82.128 | N | N | N | N |
| vg0907797330 | G -> A | LOC_Os09g13460-LOC_Os09g13470 | intergenic_region ; MODIFIER | silent_mutation | Average:70.445; most accessible tissue: Minghui63 panicle, score: 82.128 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0907797330 | NA | 1.99E-13 | Grain_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 |
| vg0907797330 | NA | 1.33E-11 | mr1486 | 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 |
| vg0907797330 | NA | 9.12E-07 | mr1543 | 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 |
| vg0907797330 | 8.85E-06 | NA | mr1585 | 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 |
| vg0907797330 | 1.81E-06 | NA | mr1672 | 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 |
| vg0907797330 | NA | 3.30E-06 | mr1672 | 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 |
| vg0907797330 | NA | 3.22E-09 | mr1543_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 |
| vg0907797330 | NA | 1.90E-06 | mr1621_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 |
| vg0907797330 | NA | 1.58E-06 | mr1680_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 |