| Variant ID: vg1209657474 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9657474 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTCAATCACCTCTCTAGGAATACCAGGCATATCGGATGGTTTACACGCAAAGATATCTTTATTATTTTGAAGAAAGGTGATAAGCGCGCTTTCCTATTTA[C/T]
AATCTAACTCAGCGCCTATTACAGCAGTCTTAGTAGGATCAGAAGGATCTAAAGGAATTTTCTTGGTCTTGGCTTCGCTTTCTCCACTCTTTGAGACCTT
AAGGTCTCAAAGAGTGGAGAAAGCGAAGCCAAGACCAAGAAAATTCCTTTAGATCCTTCTGATCCTACTAAGACTGCTGTAATAGGCGCTGAGTTAGATT[G/A]
TAAATAGGAAAGCGCGCTTATCACCTTTCTTCAAAATAATAAAGATATCTTTGCGTGTAAACCATCCGATATGCCTGGTATTCCTAGAGAGGTGATTGAG
| 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 | 93.70% | 1.10% | 1.48% | 3.68% | NA |
| All Indica | 2759 | 90.70% | 1.90% | 2.36% | 5.07% | NA |
| All Japonica | 1512 | 97.90% | 0.10% | 0.07% | 1.92% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.30% | 1.00% | 2.35% | 6.39% | NA |
| Indica II | 465 | 91.40% | 2.20% | 2.58% | 3.87% | NA |
| Indica III | 913 | 90.00% | 2.10% | 1.97% | 5.91% | NA |
| Indica Intermediate | 786 | 91.30% | 2.20% | 2.67% | 3.82% | NA |
| Temperate Japonica | 767 | 96.10% | 0.10% | 0.13% | 3.65% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 1.00% | 4.17% | 2.08% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209657474 | C -> DEL | LOC_Os12g16840.1 | N | splice_donor_variant | Average:54.197; most accessible tissue: Minghui63 flag leaf, score: 80.241 | N | N | N | N |
| vg1209657474 | C -> T | LOC_Os12g16840.1 | splice_donor_variant&intron_variant ; HIGH | splice_donor_variant | Average:54.197; most accessible tissue: Minghui63 flag leaf, score: 80.241 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209657474 | 3.53E-06 | 3.68E-06 | mr1409 | 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 |
| vg1209657474 | 8.89E-06 | NA | mr1775 | 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 |