| Variant ID: vg0610610259 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 10610259 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 101. )
TTCCTTCCCTGTTTGAAATCAGCTTATGATCGGACTTAGCGTAGCCCCTTCCCTTGACTGACGTCGTCGGACCACTCGCGGATCATCAAGTGGCGGCTTC[C/T]
CTGAAGGAGAAGGTCGTCGAGGAGGCGTCCGACATTGCCACCGGTAGTGGTGGCAAGGCTCCGACCAAGCCGAGGAAATTCTCGTCTGTGCTCGGACATC
GATGTCCGAGCACAGACGAGAATTTCCTCGGCTTGGTCGGAGCCTTGCCACCACTACCGGTGGCAATGTCGGACGCCTCCTCGACGACCTTCTCCTTCAG[G/A]
GAAGCCGCCACTTGATGATCCGCGAGTGGTCCGACGACGTCAGTCAAGGGAAGGGGCTACGCTAAGTCCGATCATAAGCTGATTTCAAACAGGGAAGGAA
| 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 | 44.50% | 4.40% | 2.71% | 48.41% | NA |
| All Indica | 2759 | 18.40% | 7.50% | 3.91% | 70.13% | NA |
| All Japonica | 1512 | 82.30% | 0.10% | 0.66% | 16.93% | NA |
| Aus | 269 | 83.30% | 0.00% | 1.12% | 15.61% | NA |
| Indica I | 595 | 14.30% | 9.20% | 3.53% | 72.94% | NA |
| Indica II | 465 | 4.30% | 4.30% | 4.30% | 87.10% | NA |
| Indica III | 913 | 25.50% | 6.00% | 3.29% | 65.17% | NA |
| Indica Intermediate | 786 | 21.80% | 9.80% | 4.71% | 63.74% | NA |
| Temperate Japonica | 767 | 87.70% | 0.10% | 0.26% | 11.86% | NA |
| Tropical Japonica | 504 | 70.40% | 0.00% | 1.39% | 28.17% | NA |
| Japonica Intermediate | 241 | 90.00% | 0.00% | 0.41% | 9.54% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 2.08% | 11.46% | NA |
| Intermediate | 90 | 44.40% | 1.10% | 5.56% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0610610259 | C -> T | LOC_Os06g18710.1 | synonymous_variant ; p.Ser272Ser; LOW | synonymous_codon | Average:18.381; most accessible tissue: Callus, score: 59.269 | N | N | N | N |
| vg0610610259 | C -> DEL | LOC_Os06g18710.1 | N | frameshift_variant | Average:18.381; most accessible tissue: Callus, score: 59.269 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0610610259 | NA | 3.53E-06 | mr1616 | 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 |
| vg0610610259 | NA | 9.69E-07 | mr1875_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 |
| vg0610610259 | NA | 1.90E-06 | mr1908_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 |