| Variant ID: vg1001287549 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1287549 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, C: 0.11, others allele: 0.00, population size: 154. )
CTGGGGAGTCCATGCCTCTAGTTTTTGAGGGGGTGACTACGATCCGGGAATAGTGCACTGCTTTGAGTTGAGTTATGTGAGGGGTCTTGTCACAATCACT[T/C]
GCCATGGTGACGTGTCTGCGCGGACACGGTGACATGACGGTGGGTTGTGTCTTGTGGGTACAGTGGTACACCTCTGGCCAGAGTAAAACTATTCGAATAG
CTATTCGAATAGTTTTACTCTGGCCAGAGGTGTACCACTGTACCCACAAGACACAACCCACCGTCATGTCACCGTGTCCGCGCAGACACGTCACCATGGC[A/G]
AGTGATTGTGACAAGACCCCTCACATAACTCAACTCAAAGCAGTGCACTATTCCCGGATCGTAGTCACCCCCTCAAAAACTAGAGGCATGGACTCCCCAG
| 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 | 70.70% | 17.30% | 11.30% | 0.76% | NA |
| All Indica | 2759 | 69.80% | 27.00% | 3.23% | 0.00% | NA |
| All Japonica | 1512 | 69.90% | 1.30% | 26.52% | 2.31% | NA |
| Aus | 269 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 79.20% | 17.50% | 3.36% | 0.00% | NA |
| Indica II | 465 | 54.40% | 39.60% | 6.02% | 0.00% | NA |
| Indica III | 913 | 68.60% | 29.50% | 1.97% | 0.00% | NA |
| Indica Intermediate | 786 | 73.30% | 23.80% | 2.93% | 0.00% | NA |
| Temperate Japonica | 767 | 87.40% | 0.50% | 9.91% | 2.22% | NA |
| Tropical Japonica | 504 | 44.80% | 2.20% | 50.99% | 1.98% | NA |
| Japonica Intermediate | 241 | 66.80% | 1.70% | 28.22% | 3.32% | NA |
| VI/Aromatic | 96 | 39.60% | 19.80% | 39.58% | 1.04% | NA |
| Intermediate | 90 | 71.10% | 22.20% | 6.67% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001287549 | T -> C | LOC_Os10g03070.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.805; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg1001287549 | T -> DEL | N | N | silent_mutation | Average:34.805; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1001287549 | NA | 9.89E-06 | mr1136 | 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 |
| vg1001287549 | 1.62E-06 | NA | mr1486 | 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 |
| vg1001287549 | 1.81E-06 | NA | mr1486 | 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 |