| Variant ID: vg0136902523 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36902523 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 47. )
TGGTTCTTCCACTATGTTCCGCTTTGACTACCCAGCTCCCCCACCGCCAGCAGCTCGTGCTGCTGCCGGCCCTCGACAGGTTCCGCCGGTCTCTTCGCGT[C/G]
AGCCGATCGACGTCTCTTCGACTGAGGAGCCGACTACAGGAGGCAGCCAGGCAGGCGAGGAGTAGAGGAGGCCGTCTTCAGCAGTTGTCCGTGTGTTAGG
CCTAACACACGGACAACTGCTGAAGACGGCCTCCTCTACTCCTCGCCTGCCTGGCTGCCTCCTGTAGTCGGCTCCTCAGTCGAAGAGACGTCGATCGGCT[G/C]
ACGCGAAGAGACCGGCGGAACCTGTCGAGGGCCGGCAGCAGCACGAGCTGCTGGCGGTGGGGGAGCTGGGTAGTCAAAGCGGAACATAGTGGAAGAACCA
| 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 | 45.10% | 41.40% | 3.24% | 10.30% | NA |
| All Indica | 2759 | 66.10% | 12.50% | 5.33% | 15.98% | NA |
| All Japonica | 1512 | 0.90% | 97.40% | 0.00% | 1.72% | NA |
| Aus | 269 | 98.90% | 0.70% | 0.37% | 0.00% | NA |
| Indica I | 595 | 75.10% | 4.20% | 9.92% | 10.76% | NA |
| Indica II | 465 | 42.80% | 4.90% | 6.24% | 46.02% | NA |
| Indica III | 913 | 73.50% | 18.90% | 1.86% | 5.70% | NA |
| Indica Intermediate | 786 | 64.60% | 15.90% | 5.34% | 14.12% | NA |
| Temperate Japonica | 767 | 0.30% | 99.10% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 1.80% | 95.00% | 0.00% | 3.17% | NA |
| Japonica Intermediate | 241 | 0.80% | 97.10% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 6.20% | 82.30% | 1.04% | 10.42% | NA |
| Intermediate | 90 | 22.20% | 62.20% | 4.44% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136902523 | C -> G | LOC_Os01g63630.1 | intron_variant ; MODIFIER | silent_mutation | Average:21.038; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0136902523 | C -> DEL | N | N | silent_mutation | Average:21.038; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0136902523 | NA | 3.28E-11 | mr1216_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 |
| vg0136902523 | NA | 9.06E-10 | mr1322_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 |
| vg0136902523 | NA | 5.11E-15 | mr1333_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 |
| vg0136902523 | NA | 5.38E-08 | mr1623_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 |
| vg0136902523 | 3.66E-06 | 1.69E-18 | mr1686_2 | 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 |