| Variant ID: vg0713017347 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 13017347 |
| Reference Allele: A | Alternative Allele: G,T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AACAAGAACTCCCCCAAGATAAAGATGAAGCCGAGCGGATTTCCAGGCGCAGCAAACTCTATGTTATTCATGAGACCGAGTTGTACAAGAAAAGTCCATC[A/G,T]
GGAATCCTGCAACGCTGTGTGTCTTTGGAGGAGGGAAGGCAATTGCTAAAAGATATACATTCAGGCATCTGTGGTAATCACGCTGCTGCACGAACCATCG
CGATGGTTCGTGCAGCAGCGTGATTACCACAGATGCCTGAATGTATATCTTTTAGCAATTGCCTTCCCTCCTCCAAAGACACACAGCGTTGCAGGATTCC[T/C,A]
GATGGACTTTTCTTGTACAACTCGGTCTCATGAATAACATAGAGTTTGCTGCGCCTGGAAATCCGCTCGGCTTCATCTTTATCTTGGGGGAGTTCTTGTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.80% | 0.10% | 11.79% | 38.17% | G: 0.06% |
| All Indica | 2759 | 28.90% | 0.20% | 15.98% | 54.87% | G: 0.07% |
| All Japonica | 1512 | 84.90% | 0.10% | 6.28% | 8.66% | G: 0.07% |
| Aus | 269 | 56.50% | 0.00% | 2.97% | 40.52% | NA |
| Indica I | 595 | 50.30% | 0.00% | 4.37% | 45.21% | G: 0.17% |
| Indica II | 465 | 20.60% | 0.00% | 21.08% | 58.06% | G: 0.22% |
| Indica III | 913 | 15.20% | 0.00% | 19.61% | 65.17% | NA |
| Indica Intermediate | 786 | 33.50% | 0.60% | 17.56% | 48.35% | NA |
| Temperate Japonica | 767 | 83.20% | 0.10% | 7.04% | 9.52% | G: 0.13% |
| Tropical Japonica | 504 | 87.30% | 0.00% | 4.17% | 8.53% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.00% | 8.30% | 6.22% | NA |
| VI/Aromatic | 96 | 72.90% | 1.00% | 6.25% | 19.79% | NA |
| Intermediate | 90 | 57.80% | 0.00% | 7.78% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0713017347 | A -> DEL | N | N | silent_mutation | Average:9.138; most accessible tissue: Callus, score: 17.081 | N | N | N | N |
| vg0713017347 | A -> G | LOC_Os07g23090.1 | upstream_gene_variant ; 3266.0bp to feature; MODIFIER | silent_mutation | Average:9.138; most accessible tissue: Callus, score: 17.081 | N | N | N | N |
| vg0713017347 | A -> G | LOC_Os07g23080.1 | downstream_gene_variant ; 1634.0bp to feature; MODIFIER | silent_mutation | Average:9.138; most accessible tissue: Callus, score: 17.081 | N | N | N | N |
| vg0713017347 | A -> G | LOC_Os07g23070.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.138; most accessible tissue: Callus, score: 17.081 | N | N | N | N |
| vg0713017347 | A -> T | LOC_Os07g23090.1 | upstream_gene_variant ; 3266.0bp to feature; MODIFIER | silent_mutation | Average:9.138; most accessible tissue: Callus, score: 17.081 | N | N | N | N |
| vg0713017347 | A -> T | LOC_Os07g23080.1 | downstream_gene_variant ; 1634.0bp to feature; MODIFIER | silent_mutation | Average:9.138; most accessible tissue: Callus, score: 17.081 | N | N | N | N |
| vg0713017347 | A -> T | LOC_Os07g23070.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.138; most accessible tissue: Callus, score: 17.081 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0713017347 | NA | 9.28E-11 | 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 |
| vg0713017347 | NA | 5.12E-10 | mr1549 | 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 |
| vg0713017347 | NA | 2.46E-09 | mr1624 | 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 |