| Variant ID: vg1215277151 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 15277151 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.16, others allele: 0.00, population size: 74. )
GTGCGGCATCGGCCTATGCAAGATGGAAATAAAAAATTCAGTAATTGTCCTATATTATGCAAGATAAATGAAATAATTGTAAGAACTAATACAAATTCGA[T/C]
GTACCCCCACGAAGTAGTCTCGGCCACGGTGCGTGGGATACGCACCCGTGACAGCGGCAACGTGCTGCTCTGGGGCGTCTGGAGTGAAGGTCACACGCGC
GCGCGTGTGACCTTCACTCCAGACGCCCCAGAGCAGCACGTTGCCGCTGTCACGGGTGCGTATCCCACGCACCGTGGCCGAGACTACTTCGTGGGGGTAC[A/G]
TCGAATTTGTATTAGTTCTTACAATTATTTCATTTATCTTGCATAATATAGGACAATTACTGAATTTTTTATTTCCATCTTGCATAGGCCGATGCCGCAC
| 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 | 35.10% | 17.10% | 11.66% | 36.16% | NA |
| All Indica | 2759 | 6.20% | 26.90% | 8.19% | 58.72% | NA |
| All Japonica | 1512 | 76.50% | 3.80% | 16.40% | 3.31% | NA |
| Aus | 269 | 89.60% | 0.00% | 8.18% | 2.23% | NA |
| Indica I | 595 | 4.90% | 8.20% | 6.39% | 80.50% | NA |
| Indica II | 465 | 5.80% | 55.90% | 12.26% | 26.02% | NA |
| Indica III | 913 | 4.60% | 21.60% | 7.56% | 66.27% | NA |
| Indica Intermediate | 786 | 9.30% | 30.00% | 7.89% | 52.80% | NA |
| Temperate Japonica | 767 | 93.70% | 0.80% | 3.65% | 1.83% | NA |
| Tropical Japonica | 504 | 52.80% | 9.50% | 34.13% | 3.57% | NA |
| Japonica Intermediate | 241 | 71.40% | 1.20% | 19.92% | 7.47% | NA |
| VI/Aromatic | 96 | 41.70% | 1.00% | 42.71% | 14.58% | NA |
| Intermediate | 90 | 55.60% | 7.80% | 15.56% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1215277151 | T -> C | LOC_Os12g26204.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:16.792; most accessible tissue: Minghui63 young leaf, score: 29.964 | N | N | N | N |
| vg1215277151 | T -> C | LOC_Os12g26190.1 | downstream_gene_variant ; 4609.0bp to feature; MODIFIER | silent_mutation | Average:16.792; most accessible tissue: Minghui63 young leaf, score: 29.964 | N | N | N | N |
| vg1215277151 | T -> DEL | N | N | silent_mutation | Average:16.792; most accessible tissue: Minghui63 young leaf, score: 29.964 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1215277151 | 5.57E-06 | NA | mr1383 | 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 |
| vg1215277151 | 3.00E-06 | 3.00E-06 | mr1564 | 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 |
| vg1215277151 | NA | 6.19E-06 | mr1712 | 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 |
| vg1215277151 | NA | 9.66E-06 | mr1866 | 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 |
| vg1215277151 | NA | 6.39E-06 | mr1884 | 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 |