| Variant ID: vg1006615974 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 6615974 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 89. )
AACAGCTGCCGTCTGTACTTTGGTCCTTGCGCACCACTCCCAGTCGGGCCATGGGCCAGTCGCCGTTTTTCTTAGTTTATGGAGCGGAAGCAATGTGGCC[C/T]
AGTGAGGTGGAATTTGAATCTTTACGTTTTCGCAACTTTAACGAGGAGCGCTACGGAGAAGACCGAGTAGATGATTTGAACTGACTGGAAGAGGCCCTCG
CGAGGGCCTCTTCCAGTCAGTTCAAATCATCTACTCGGTCTTCTCCGTAGCGCTCCTCGTTAAAGTTGCGAAAACGTAAAGATTCAAATTCCACCTCACT[G/A]
GGCCACATTGCTTCCGCTCCATAAACTAAGAAAAACGGCGACTGGCCCATGGCCCGACTGGGAGTGGTGCGCAAGGACCAAAGTACAGACGGCAGCTGTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.30% | 20.40% | 2.84% | 52.48% | NA |
| All Indica | 2759 | 38.10% | 2.80% | 3.26% | 55.85% | NA |
| All Japonica | 1512 | 1.00% | 56.50% | 0.13% | 42.33% | NA |
| Aus | 269 | 20.80% | 1.10% | 14.87% | 63.20% | NA |
| Indica I | 595 | 12.40% | 6.10% | 4.03% | 77.48% | NA |
| Indica II | 465 | 60.90% | 2.40% | 0.22% | 36.56% | NA |
| Indica III | 913 | 38.80% | 0.80% | 5.59% | 54.87% | NA |
| Indica Intermediate | 786 | 43.40% | 2.80% | 1.78% | 52.04% | NA |
| Temperate Japonica | 767 | 0.50% | 88.70% | 0.00% | 10.82% | NA |
| Tropical Japonica | 504 | 0.60% | 8.50% | 0.40% | 90.48% | NA |
| Japonica Intermediate | 241 | 3.30% | 54.80% | 0.00% | 41.91% | NA |
| VI/Aromatic | 96 | 5.20% | 6.20% | 0.00% | 88.54% | NA |
| Intermediate | 90 | 23.30% | 25.60% | 2.22% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1006615974 | C -> T | LOC_Os10g11920.1 | synonymous_variant ; p.Pro981Pro; LOW | synonymous_codon | Average:16.01; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
| vg1006615974 | C -> DEL | LOC_Os10g11920.1 | N | frameshift_variant | Average:16.01; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1006615974 | NA | 7.51E-08 | mr1552 | 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 |
| vg1006615974 | NA | 4.83E-09 | mr1090_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 |
| vg1006615974 | NA | 1.14E-07 | mr1211_2 | 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 |