| Variant ID: vg0525619564 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 25619564 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TAGCAACCAGTTTGAAATATGGAAATACTCCTACGGGAGTGTTTAGTTTACACCAAAATTAAAAGTTTGGTTGAAATTAGAACGATGTGATGGAAAAGTT[G/A]
AAAGTTTATGTGTGTATGAAAGTTTTGATGTGATAGAAAAGTCGGAAGTTTGAAAAAATATTTTGAAACTAAACACGGCCTATGTATATGAAGTCCACGT
ACGTGGACTTCATATACATAGGCCGTGTTTAGTTTCAAAATATTTTTTCAAACTTCCGACTTTTCTATCACATCAAAACTTTCATACACACATAAACTTT[C/T]
AACTTTTCCATCACATCGTTCTAATTTCAACCAAACTTTTAATTTTGGTGTAAACTAAACACTCCCGTAGGAGTATTTCCATATTTCAAACTGGTTGCTA
| 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 | 94.30% | 3.60% | 2.12% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.20% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 84.60% | 9.30% | 6.15% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 88.50% | 2.90% | 8.60% | 0.00% | NA |
| Tropical Japonica | 504 | 94.00% | 4.80% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 52.30% | 39.00% | 8.71% | 0.00% | NA |
| VI/Aromatic | 96 | 75.00% | 21.90% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 3.30% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0525619564 | G -> A | LOC_Os05g44050.1 | upstream_gene_variant ; 987.0bp to feature; MODIFIER | silent_mutation | Average:46.182; most accessible tissue: Callus, score: 79.734 | N | N | N | N |
| vg0525619564 | G -> A | LOC_Os05g44060.1 | upstream_gene_variant ; 4459.0bp to feature; MODIFIER | silent_mutation | Average:46.182; most accessible tissue: Callus, score: 79.734 | N | N | N | N |
| vg0525619564 | G -> A | LOC_Os05g44030.1 | downstream_gene_variant ; 1263.0bp to feature; MODIFIER | silent_mutation | Average:46.182; most accessible tissue: Callus, score: 79.734 | N | N | N | N |
| vg0525619564 | G -> A | LOC_Os05g44030-LOC_Os05g44050 | intergenic_region ; MODIFIER | silent_mutation | Average:46.182; most accessible tissue: Callus, score: 79.734 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0525619564 | 2.18E-06 | NA | Plant_height | Jap_All | YES | 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 |
| vg0525619564 | NA | 6.43E-06 | mr1180 | 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 |
| vg0525619564 | NA | 3.24E-07 | mr1180_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 |
| vg0525619564 | NA | 4.46E-07 | mr1183_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 |