| Variant ID: vg0620614935 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20614935 |
| 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: 104. )
ATGGGGACGTTGTCTCTCACGACCCAACCACAATGATTCACAAACTTTCGTCCTATACCCGTCGGGGCTACTGGTTCGCCGTCTGGGGCAATCTCAGTAA[C/T]
GATGTGCCTTCCCTCAAGCTTCATCGCGGGACCTCTTTTCCCACGTGGCCTCTTCTGTCCGGCCGACGGTTGACTATCAATCCCCTCCTCGGTCCCCTCC
GGAGGGGACCGAGGAGGGGATTGATAGTCAACCGTCGGCCGGACAGAAGAGGCCACGTGGGAAAAGAGGTCCCGCGATGAAGCTTGAGGGAAGGCACATC[G/A]
TTACTGAGATTGCCCCAGACGGCGAACCAGTAGCCCCGACGGGTATAGGACGAAAGTTTGTGAATCATTGTGGTTGGGTCGTGAGAGACAACGTCCCCAT
| 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 | 37.70% | 12.70% | 10.54% | 39.04% | NA |
| All Indica | 2759 | 8.10% | 11.70% | 16.20% | 63.94% | NA |
| All Japonica | 1512 | 94.00% | 0.90% | 1.52% | 3.57% | NA |
| Aus | 269 | 13.40% | 81.80% | 4.09% | 0.74% | NA |
| Indica I | 595 | 5.40% | 0.80% | 7.73% | 86.05% | NA |
| Indica II | 465 | 6.70% | 3.70% | 20.65% | 69.03% | NA |
| Indica III | 913 | 8.20% | 24.10% | 20.15% | 47.54% | NA |
| Indica Intermediate | 786 | 10.90% | 10.40% | 15.39% | 63.23% | NA |
| Temperate Japonica | 767 | 96.90% | 0.00% | 0.78% | 2.35% | NA |
| Tropical Japonica | 504 | 91.30% | 2.60% | 2.78% | 3.37% | NA |
| Japonica Intermediate | 241 | 90.90% | 0.00% | 1.24% | 7.88% | NA |
| VI/Aromatic | 96 | 55.20% | 33.30% | 8.33% | 3.12% | NA |
| Intermediate | 90 | 52.20% | 13.30% | 10.00% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620614935 | C -> T | LOC_Os06g35350.1 | missense_variant ; p.Val9Ile; MODERATE | nonsynonymous_codon ; V9I | Average:13.394; most accessible tissue: Callus, score: 37.552 | unknown | unknown | TOLERATED | 1.00 |
| vg0620614935 | C -> DEL | LOC_Os06g35350.1 | N | frameshift_variant | Average:13.394; most accessible tissue: Callus, score: 37.552 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0620614935 | NA | 4.65E-08 | mr1392 | 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 |
| vg0620614935 | 4.70E-06 | 4.70E-06 | mr1392 | Ind_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 |