| Variant ID: vg1221303134 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21303134 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 200. )
CTCTAACAAACACCTTGCATGCATCGAACAGTGCACGGTGTGAGAAGGAAAAAGCAGAGCTCCTAAAACAGAGCTCCATAGTGCCAGCTTATATCATCAA[G/C]
TCTAACATTCTCCCCCTAAGCCTGGCACCGTGAACTGACCTCGACGACGCTGATGCGAGCTCGCAATTCTTGAAAACGAACCCGCCCGAGTGCCTTGGTC
GACCAAGGCACTCGGGCGGGTTCGTTTTCAAGAATTGCGAGCTCGCATCAGCGTCGTCGAGGTCAGTTCACGGTGCCAGGCTTAGGGGGAGAATGTTAGA[C/G]
TTGATGATATAAGCTGGCACTATGGAGCTCTGTTTTAGGAGCTCTGCTTTTTCCTTCTCACACCGTGCACTGTTCGATGCATGCAAGGTGTTTGTTAGAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.80% | 6.70% | 1.42% | 8.08% | NA |
| All Indica | 2759 | 76.20% | 9.50% | 2.07% | 12.29% | NA |
| All Japonica | 1512 | 99.50% | 0.40% | 0.07% | 0.00% | NA |
| Aus | 269 | 68.80% | 14.50% | 2.60% | 14.13% | NA |
| Indica I | 595 | 83.40% | 8.40% | 2.02% | 6.22% | NA |
| Indica II | 465 | 81.10% | 9.00% | 2.80% | 7.10% | NA |
| Indica III | 913 | 64.70% | 12.70% | 1.42% | 21.14% | NA |
| Indica Intermediate | 786 | 81.20% | 6.70% | 2.42% | 9.67% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 4.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 6.70% | 1.11% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221303134 | G -> C | LOC_Os12g35000.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.591; most accessible tissue: Zhenshan97 young leaf, score: 87.443 | N | N | N | N |
| vg1221303134 | G -> DEL | N | N | silent_mutation | Average:64.591; most accessible tissue: Zhenshan97 young leaf, score: 87.443 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1221303134 | NA | 9.78E-06 | mr1042 | 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 |
| vg1221303134 | 2.82E-06 | NA | mr1758 | 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 |