| Variant ID: vg1010137144 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 10137144 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 104. )
ATTCTTCTTCCGAGTGATTACTCCACTGGACTTTGCAAAAACGGATAACTCGATTCCTGGTTCTTCTCTCACTTGTTTCCAGGATACGGATTGGTTTCTC[A/C]
ACATAAGTCAAATCCTCTTGGACTTCTATCTGGTCAAGATTAGCTTGTTCGGTAGGTACCCTTAAACACTTTTTCAATTGCGAAACATGGAACACATTAT
ATAATGTGTTCCATGTTTCGCAATTGAAAAAGTGTTTAAGGGTACCTACCGAACAAGCTAATCTTGACCAGATAGAAGTCCAAGAGGATTTGACTTATGT[T/G]
GAGAAACCAATCCGTATCCTGGAAACAAGTGAGAGAAGAACCAGGAATCGAGTTATCCGTTTTTGCAAAGTCCAGTGGAGTAATCACTCGGAAGAAGAAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 14.90% | 0.80% | 8.10% | 76.20% | NA |
| All Indica | 2759 | 2.20% | 0.70% | 6.27% | 90.79% | NA |
| All Japonica | 1512 | 41.10% | 0.70% | 8.80% | 49.40% | NA |
| Aus | 269 | 0.00% | 1.10% | 4.09% | 94.80% | NA |
| Indica I | 595 | 2.00% | 0.00% | 3.53% | 94.45% | NA |
| Indica II | 465 | 2.20% | 1.50% | 5.38% | 90.97% | NA |
| Indica III | 913 | 1.60% | 0.40% | 9.09% | 88.83% | NA |
| Indica Intermediate | 786 | 3.20% | 1.00% | 5.60% | 90.20% | NA |
| Temperate Japonica | 767 | 56.70% | 0.30% | 8.21% | 34.81% | NA |
| Tropical Japonica | 504 | 12.90% | 1.40% | 11.71% | 74.01% | NA |
| Japonica Intermediate | 241 | 50.60% | 0.40% | 4.56% | 44.40% | NA |
| VI/Aromatic | 96 | 1.00% | 4.20% | 56.25% | 38.54% | NA |
| Intermediate | 90 | 23.30% | 0.00% | 13.33% | 63.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1010137144 | A -> C | LOC_Os10g20190.1 | synonymous_variant ; p.Val1621Val; LOW | synonymous_codon | Average:5.844; most accessible tissue: Callus, score: 16.646 | N | N | N | N |
| vg1010137144 | A -> DEL | LOC_Os10g20190.1 | N | frameshift_variant | Average:5.844; most accessible tissue: Callus, score: 16.646 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1010137144 | 8.14E-07 | 6.57E-08 | mr1201 | 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 |
| vg1010137144 | NA | 3.77E-06 | mr1219 | 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 |
| vg1010137144 | NA | 3.34E-06 | mr1167_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 |
| vg1010137144 | 1.77E-07 | 1.77E-07 | mr1950_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 |