| Variant ID: vg0128139083 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28139083 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.03, others allele: 0.00, population size: 117. )
CTAATATTCCTTACTCCCTCCGTCCCAAAAAAAGACAAATCCTGGTTTCCGTGTCCAACGTTTGACCGTCCGTCTTATTTGGAAAAATTATGAAAAAAAA[T/A]
TAAAAAGACAAGTCACGCATAAAATATTAATCATGTTTTATCATCTAACAACAATGAAAATACGAATTATAAAAAAATTTCATATAAGACGGACAGTCAA
TTGACTGTCCGTCTTATATGAAATTTTTTTATAATTCGTATTTTCATTGTTGTTAGATGATAAAACATGATTAATATTTTATGCGTGACTTGTCTTTTTA[A/T]
TTTTTTTTCATAATTTTTCCAAATAAGACGGACGGTCAAACGTTGGACACGGAAACCAGGATTTGTCTTTTTTTGGGACGGAGGGAGTAAGGAATATTAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.30% | 45.30% | 0.32% | 0.06% | NA |
| All Indica | 2759 | 30.50% | 68.90% | 0.54% | 0.11% | NA |
| All Japonica | 1512 | 87.40% | 12.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 91.80% | 8.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 34.60% | 64.20% | 1.18% | 0.00% | NA |
| Indica II | 465 | 58.90% | 40.20% | 0.65% | 0.22% | NA |
| Indica III | 913 | 6.50% | 93.20% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 38.40% | 61.10% | 0.38% | 0.13% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 64.50% | 35.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 31.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128139083 | T -> A | LOC_Os01g49000.1 | intron_variant ; MODIFIER | silent_mutation | Average:23.893; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0128139083 | T -> DEL | N | N | silent_mutation | Average:23.893; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0128139083 | NA | 8.65E-06 | mr1596 | 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 |
| vg0128139083 | 1.90E-06 | 2.40E-10 | mr1550_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 |