| Variant ID: vg0816207758 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 16207758 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCACTGATAAAGTTCACAGGTGCAGGTATGGTTGTGAATAATTTATATGCTTGATTTATATCTTGAAGAAATTCATTCTACACTAACGTTTACTCAGGGA[C/T]
GAGCAAAGGGCTAAGTGTGGGGGGTTTTGTTGGCGGCTGTTAAATGCCAATTCTATACCGCCAACATCTGCATAAAGTTCAGATAATAAAACATCCAACA
TGTTGGATGTTTTATTATCTGAACTTTATGCAGATGTTGGCGGTATAGAATTGGCATTTAACAGCCGCCAACAAAACCCCCCACACTTAGCCCTTTGCTC[G/A]
TCCCTGAGTAAACGTTAGTGTAGAATGAATTTCTTCAAGATATAAATCAAGCATATAAATTATTCACAACCATACCTGCACCTGTGAACTTTATCAGTGG
| 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 | 60.00% | 15.20% | 20.00% | 4.85% | NA |
| All Indica | 2759 | 56.10% | 17.00% | 23.99% | 2.90% | NA |
| All Japonica | 1512 | 65.00% | 15.10% | 11.44% | 8.40% | NA |
| Aus | 269 | 57.20% | 1.10% | 34.94% | 6.69% | NA |
| Indica I | 595 | 75.00% | 4.50% | 18.32% | 2.18% | NA |
| Indica II | 465 | 42.80% | 26.20% | 28.17% | 2.80% | NA |
| Indica III | 913 | 50.70% | 21.80% | 23.55% | 3.94% | NA |
| Indica Intermediate | 786 | 55.90% | 15.50% | 26.34% | 2.29% | NA |
| Temperate Japonica | 767 | 97.30% | 1.80% | 0.65% | 0.26% | NA |
| Tropical Japonica | 504 | 25.60% | 24.40% | 27.58% | 22.42% | NA |
| Japonica Intermediate | 241 | 44.80% | 38.20% | 12.03% | 4.98% | NA |
| VI/Aromatic | 96 | 94.80% | 1.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 67.80% | 14.40% | 15.56% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0816207758 | C -> T | LOC_Os08g26670.1 | upstream_gene_variant ; 2126.0bp to feature; MODIFIER | silent_mutation | Average:25.382; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0816207758 | C -> T | LOC_Os08g26650.1 | downstream_gene_variant ; 4538.0bp to feature; MODIFIER | silent_mutation | Average:25.382; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0816207758 | C -> T | LOC_Os08g26660.1 | downstream_gene_variant ; 1641.0bp to feature; MODIFIER | silent_mutation | Average:25.382; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0816207758 | C -> T | LOC_Os08g26680.1 | downstream_gene_variant ; 4960.0bp to feature; MODIFIER | silent_mutation | Average:25.382; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0816207758 | C -> T | LOC_Os08g26660-LOC_Os08g26670 | intergenic_region ; MODIFIER | silent_mutation | Average:25.382; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0816207758 | C -> DEL | N | N | silent_mutation | Average:25.382; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0816207758 | NA | 9.79E-06 | mr1286 | 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 |
| vg0816207758 | NA | 5.40E-06 | mr1519 | 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 |
| vg0816207758 | 1.33E-06 | 1.33E-06 | mr1777 | 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 |
| vg0816207758 | NA | 2.13E-06 | mr1519_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 |