| Variant ID: vg1125485978 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25485978 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAAGTGAAGTTGAATTCGAGTCTTTGCGCTTTCGAAATTTCCGTGAAGAACGCTACGATGAGGACCGAGTGGATGACTTGCACCGATTGGAGGAAGTCCG[C/T]
GAAGCAGCTTTAATTCGGTCGGCTCGATACTTACAAGGGTTGCGGCGTTATCATAATCGCAATGTTCGATCCCGTGCCTTTTTAGTCGGCGACCTGGTTT
AAACCAGGTCGCCGACTAAAAAGGCACGGGATCGAACATTGCGATTATGATAACGCCGCAACCCTTGTAAGTATCGAGCCGACCGAATTAAAGCTGCTTC[G/A]
CGGACTTCCTCCAATCGGTGCAAGTCATCCACTCGGTCCTCATCGTAGCGTTCTTCACGGAAATTTCGAAAGCGCAAAGACTCGAATTCAACTTCACTTG
| 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 | 56.90% | 4.50% | 24.57% | 14.03% | NA |
| All Indica | 2759 | 46.80% | 0.10% | 33.42% | 19.75% | NA |
| All Japonica | 1512 | 69.00% | 13.60% | 11.11% | 6.28% | NA |
| Aus | 269 | 79.20% | 0.00% | 15.99% | 4.83% | NA |
| Indica I | 595 | 75.00% | 0.00% | 5.55% | 19.50% | NA |
| Indica II | 465 | 67.10% | 0.40% | 8.39% | 24.09% | NA |
| Indica III | 913 | 13.50% | 0.00% | 71.19% | 15.33% | NA |
| Indica Intermediate | 786 | 52.00% | 0.00% | 25.45% | 22.52% | NA |
| Temperate Japonica | 767 | 69.50% | 22.90% | 5.22% | 2.35% | NA |
| Tropical Japonica | 504 | 63.90% | 1.00% | 22.22% | 12.90% | NA |
| Japonica Intermediate | 241 | 78.40% | 10.00% | 6.64% | 4.98% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 14.58% | 3.12% | NA |
| Intermediate | 90 | 67.80% | 8.90% | 15.56% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125485978 | C -> T | LOC_Os11g42320.1 | synonymous_variant ; p.Arg1906Arg; LOW | synonymous_codon | Average:19.287; most accessible tissue: Zhenshan97 flag leaf, score: 50.663 | N | N | N | N |
| vg1125485978 | C -> DEL | LOC_Os11g42320.1 | N | frameshift_variant | Average:19.287; most accessible tissue: Zhenshan97 flag leaf, score: 50.663 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125485978 | 1.98E-06 | NA | mr1484 | 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 |
| vg1125485978 | 1.68E-06 | NA | mr1900 | 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 |
| vg1125485978 | 2.69E-08 | 1.84E-12 | mr1530_2 | 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 |