| Variant ID: vg0119127859 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 19127859 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.61, T: 0.39, others allele: 0.00, population size: 108. )
TGATTCATGTCCTCCAACCACAAAACTGGGTATATCAACCACTCCAACTATCAAAACCGGTGCAAACAATGTCCCTCAGTGGTTTTGGCTGACGTGGCGC[T/C]
TACGTGTCATTCTTGACCGAACCTTTGTCCTACGTGCTGCTTACGTGGCATTAGAATAAAAACAGAAATAAAAGAAATATGTGGGACCCATATATCATTC
GAATGATATATGGGTCCCACATATTTCTTTTATTTCTGTTTTTATTCTAATGCCACGTAAGCAGCACGTAGGACAAAGGTTCGGTCAAGAATGACACGTA[A/G]
GCGCCACGTCAGCCAAAACCACTGAGGGACATTGTTTGCACCGGTTTTGATAGTTGGAGTGGTTGATATACCCAGTTTTGTGGTTGGAGGACATGAATCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.30% | 21.50% | 0.57% | 26.62% | NA |
| All Indica | 2759 | 18.90% | 36.10% | 0.98% | 43.97% | NA |
| All Japonica | 1512 | 97.80% | 0.10% | 0.00% | 2.12% | NA |
| Aus | 269 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 6.10% | 79.00% | 0.34% | 14.62% | NA |
| Indica II | 465 | 32.00% | 21.10% | 1.08% | 45.81% | NA |
| Indica III | 913 | 17.70% | 17.10% | 0.99% | 64.18% | NA |
| Indica Intermediate | 786 | 22.30% | 34.70% | 1.40% | 41.60% | NA |
| Temperate Japonica | 767 | 99.20% | 0.10% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 95.20% | 0.00% | 0.00% | 4.76% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 71.10% | 14.40% | 0.00% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0119127859 | T -> DEL | N | N | silent_mutation | Average:32.728; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 | N | N | N | N |
| vg0119127859 | T -> C | LOC_Os01g34690.1 | downstream_gene_variant ; 2109.0bp to feature; MODIFIER | silent_mutation | Average:32.728; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 | N | N | N | N |
| vg0119127859 | T -> C | LOC_Os01g34680.1 | intron_variant ; MODIFIER | silent_mutation | Average:32.728; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0119127859 | NA | 2.88E-07 | mr1446_2 | 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 |
| vg0119127859 | 1.16E-06 | NA | mr1448_2 | 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 |
| vg0119127859 | 2.34E-08 | 8.98E-11 | mr1448_2 | 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 |
| vg0119127859 | NA | 1.12E-06 | mr1910_2 | 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 |