| Variant ID: vg0202324015 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2324015 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.57, C: 0.43, others allele: 0.00, population size: 51. )
TTGTCCAAAGCATATGCAATCTCTCTCTGACCACGTACTCATGATCGAGACCGAGCCGAGCGAGAGGAGAGAAAGGCGAGGGAAGGGACGACCACATTAG[T/C]
ATCGTCACTCACTAGACACGTTGCCACCTTCCCCCACTATCCACGAAAGATGTGGTGAAAGGAGGCAGGAGATATTGCTCGAGTAGGTTGCTGCTTCTTG
CAAGAAGCAGCAACCTACTCGAGCAATATCTCCTGCCTCCTTTCACCACATCTTTCGTGGATAGTGGGGGAAGGTGGCAACGTGTCTAGTGAGTGACGAT[A/G]
CTAATGTGGTCGTCCCTTCCCTCGCCTTTCTCTCCTCTCGCTCGGCTCGGTCTCGATCATGAGTACGTGGTCAGAGAGAGATTGCATATGCTTTGGACAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.80% | 39.60% | 0.23% | 16.31% | NA |
| All Indica | 2759 | 65.20% | 31.90% | 0.11% | 2.75% | NA |
| All Japonica | 1512 | 1.20% | 55.60% | 0.40% | 42.86% | NA |
| Aus | 269 | 83.60% | 5.90% | 0.00% | 10.41% | NA |
| Indica I | 595 | 72.60% | 20.70% | 0.17% | 6.55% | NA |
| Indica II | 465 | 73.80% | 25.60% | 0.00% | 0.65% | NA |
| Indica III | 913 | 52.20% | 45.80% | 0.11% | 1.86% | NA |
| Indica Intermediate | 786 | 69.70% | 28.00% | 0.13% | 2.16% | NA |
| Temperate Japonica | 767 | 0.30% | 89.00% | 0.13% | 10.56% | NA |
| Tropical Japonica | 504 | 2.40% | 11.10% | 0.79% | 85.71% | NA |
| Japonica Intermediate | 241 | 1.70% | 41.90% | 0.41% | 56.02% | NA |
| VI/Aromatic | 96 | 3.10% | 95.80% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 28.90% | 48.90% | 2.22% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202324015 | T -> DEL | N | N | silent_mutation | Average:70.961; most accessible tissue: Callus, score: 84.123 | N | N | N | N |
| vg0202324015 | T -> C | LOC_Os02g04950.1 | upstream_gene_variant ; 678.0bp to feature; MODIFIER | silent_mutation | Average:70.961; most accessible tissue: Callus, score: 84.123 | N | N | N | N |
| vg0202324015 | T -> C | LOC_Os02g04960.1 | upstream_gene_variant ; 1399.0bp to feature; MODIFIER | silent_mutation | Average:70.961; most accessible tissue: Callus, score: 84.123 | N | N | N | N |
| vg0202324015 | T -> C | LOC_Os02g04950-LOC_Os02g04960 | intergenic_region ; MODIFIER | silent_mutation | Average:70.961; most accessible tissue: Callus, score: 84.123 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0202324015 | NA | 3.59E-06 | mr1156 | 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 |
| vg0202324015 | NA | 1.66E-07 | mr1383_2 | 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 |
| vg0202324015 | NA | 1.93E-06 | mr1715_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 |