| Variant ID: vg0114527004 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14527004 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )
AAAAGGTTACTATCATGTGCGGATTGCATATTTCCAAGTCTTTGGCTTCATTAATTTTGGCCCTGGTCACAGATGATGATGTTGGAAGACATACGTATAA[G/T]
TTAATGTACCATGAAAAATATAAATCTATATATAGGCATTACACAAAAAGTATCATAGTATATATCTTGAGTAGGGAACTATTACAAACTAATTTCATGA
TCATGAAATTAGTTTGTAATAGTTCCCTACTCAAGATATATACTATGATACTTTTTGTGTAATGCCTATATATAGATTTATATTTTTCATGGTACATTAA[C/A]
TTATACGTATGTCTTCCAACATCATCATCTGTGACCAGGGCCAAAATTAATGAAGCCAAAGACTTGGAAATATGCAATCCGCACATGATAGTAACCTTTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.90% | 4.30% | 0.44% | 3.34% | NA |
| All Indica | 2759 | 86.30% | 7.40% | 0.76% | 5.62% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 71.10% | 24.40% | 0.34% | 4.20% | NA |
| Indica II | 465 | 94.40% | 3.00% | 0.00% | 2.58% | NA |
| Indica III | 913 | 92.30% | 0.10% | 0.99% | 6.57% | NA |
| Indica Intermediate | 786 | 85.90% | 5.50% | 1.27% | 7.38% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114527004 | G -> T | LOC_Os01g25630.1 | intron_variant ; MODIFIER | silent_mutation | Average:49.075; most accessible tissue: Callus, score: 80.0 | N | N | N | N |
| vg0114527004 | G -> DEL | N | N | silent_mutation | Average:49.075; most accessible tissue: Callus, score: 80.0 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0114527004 | NA | 9.86E-07 | mr1519 | Ind_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 |
| vg0114527004 | 1.64E-06 | 3.87E-10 | mr1519_2 | Ind_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 |