| Variant ID: vg0620535795 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20535795 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.90, C: 0.11, others allele: 0.00, population size: 90. )
GAAGAGGATCCAGCGAGCACACCCCACCATTCCCCCTTTGTCACCACCTTGCACCACCGTTTCTTGTTTTCGTTGCTGTTTGGGTTTGTGTTTTGTGGCG[T/C]
CCTTTGTGGTTAGACTCGTGTCTCTACTTCGACTAGCCTAGGACCAGCACTGTACACTATACCCTTGAGCGATTATTCAATTTGCTTTGGCTAATGTGGT
ACCACATTAGCCAAAGCAAATTGAATAATCGCTCAAGGGTATAGTGTACAGTGCTGGTCCTAGGCTAGTCGAAGTAGAGACACGAGTCTAACCACAAAGG[A/G]
CGCCACAAAACACAAACCCAAACAGCAACGAAAACAAGAAACGGTGGTGCAAGGTGGTGACAAAGGGGGAATGGTGGGGTGTGCTCGCTGGATCCTCTTC
| 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 | 57.60% | 34.80% | 6.03% | 1.59% | NA |
| All Indica | 2759 | 84.10% | 3.40% | 9.82% | 2.61% | NA |
| All Japonica | 1512 | 3.50% | 95.80% | 0.46% | 0.20% | NA |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 82.40% | 3.90% | 10.42% | 3.36% | NA |
| Indica II | 465 | 76.80% | 4.90% | 13.76% | 4.52% | NA |
| Indica III | 913 | 88.70% | 1.50% | 8.32% | 1.42% | NA |
| Indica Intermediate | 786 | 84.50% | 4.50% | 8.78% | 2.29% | NA |
| Temperate Japonica | 767 | 2.20% | 97.00% | 0.52% | 0.26% | NA |
| Tropical Japonica | 504 | 6.20% | 93.10% | 0.60% | 0.20% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 44.80% | 54.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 43.30% | 50.00% | 6.67% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620535795 | T -> C | LOC_Os06g35210.1 | intron_variant ; MODIFIER | silent_mutation | Average:18.086; most accessible tissue: Zhenshan97 flower, score: 28.855 | N | N | N | N |
| vg0620535795 | T -> DEL | N | N | silent_mutation | Average:18.086; most accessible tissue: Zhenshan97 flower, score: 28.855 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0620535795 | NA | 3.20E-08 | mr1082 | Ind_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 |
| vg0620535795 | NA | 3.39E-06 | mr1083 | Ind_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 |
| vg0620535795 | NA | 2.93E-06 | mr1176 | Ind_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 |
| vg0620535795 | NA | 3.80E-15 | mr1361 | 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 |
| vg0620535795 | NA | 3.29E-06 | mr1408 | 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 |
| vg0620535795 | 5.78E-07 | 6.17E-08 | mr1408 | 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 |
| vg0620535795 | NA | 9.58E-12 | mr1949 | 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 |