| Variant ID: vg0912300788 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 12300788 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATCTAAAACTTTTATTTTGGTCATTTCTTCATACGACAAAGTGATAGTAACATTGTTCACAAAATTGACATATCTCTTATCTAGTTTTATAAACTATAA[T/C]
ACATATATGTAAATTTATAAATAATATTACTAACATTTCGTCAGATAAAGAAATAACAAAAATAAAAGTTTTAGATCTTGATGAGTTATTCAACTTTGTT
AACAAAGTTGAATAACTCATCAAGATCTAAAACTTTTATTTTTGTTATTTCTTTATCTGACGAAATGTTAGTAATATTATTTATAAATTTACATATATGT[A/G]
TTATAGTTTATAAAACTAGATAAGAGATATGTCAATTTTGTGAACAATGTTACTATCACTTTGTCGTATGAAGAAATGACCAAAATAAAAGTTTTAGATC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.60% | 41.50% | 7.64% | 3.28% | NA |
| All Indica | 2759 | 74.00% | 7.90% | 12.65% | 5.40% | NA |
| All Japonica | 1512 | 4.20% | 95.20% | 0.46% | 0.20% | NA |
| Aus | 269 | 36.40% | 62.80% | 0.37% | 0.37% | NA |
| Indica I | 595 | 55.00% | 6.10% | 29.24% | 9.75% | NA |
| Indica II | 465 | 74.00% | 10.10% | 9.68% | 6.24% | NA |
| Indica III | 913 | 87.10% | 7.30% | 3.61% | 1.97% | NA |
| Indica Intermediate | 786 | 73.40% | 8.70% | 12.34% | 5.60% | NA |
| Temperate Japonica | 767 | 1.00% | 98.00% | 0.52% | 0.39% | NA |
| Tropical Japonica | 504 | 9.30% | 90.50% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 3.30% | 95.90% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 18.80% | 81.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 30.00% | 63.30% | 4.44% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0912300788 | T -> DEL | N | N | silent_mutation | Average:10.622; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0912300788 | T -> C | LOC_Os09g20440.1 | upstream_gene_variant ; 2599.0bp to feature; MODIFIER | silent_mutation | Average:10.622; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0912300788 | T -> C | LOC_Os09g20440-LOC_Os09g20450 | intergenic_region ; MODIFIER | silent_mutation | Average:10.622; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0912300788 | NA | 3.62E-10 | mr1151 | 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 |
| vg0912300788 | NA | 3.66E-08 | mr1249 | 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 |
| vg0912300788 | NA | 2.67E-09 | mr1827 | 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 |
| vg0912300788 | 1.73E-06 | NA | mr1912 | 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 |
| vg0912300788 | NA | 9.47E-09 | mr1940_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 |