| Variant ID: vg0811932078 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11932078 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGGGGGGTCATGCAAGAGGTTTTCAGGTAAATTCGGCTAAAATTATCAATAAGTATCAGAAGAGGTATGACAAACAACAGGAGAGGCGTTATGAAGAAGG[T/C]
GATGACGGTTTTGATCCTCATTGGGGCTGCGAGTTCTTTAGATTTTGCTGGAATGAGGGTATGAGGTTGCCATCTATCGAGGACTGTCCTGGGTGCGGTA
TACCGCACCCAGGACAGTCCTCGATAGATGGCAACCTCATACCCTCATTCCAGCAAAATCTAAAGAACTCGCAGCCCCAATGAGGATCAAAACCGTCATC[A/G]
CCTTCTTCATAACGCCTCTCCTGTTGTTTGTCATACCTCTTCTGATACTTATTGATAATTTTAGCCGAATTTACCTGAAAACCTCTTGCATGACCCCCCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.10% | 3.00% | 24.16% | 11.79% | NA |
| All Indica | 2759 | 54.10% | 5.00% | 33.67% | 7.18% | NA |
| All Japonica | 1512 | 71.00% | 0.00% | 9.26% | 19.71% | NA |
| Aus | 269 | 84.40% | 0.40% | 14.50% | 0.74% | NA |
| Indica I | 595 | 46.70% | 4.90% | 40.67% | 7.73% | NA |
| Indica II | 465 | 50.30% | 7.70% | 36.56% | 5.38% | NA |
| Indica III | 913 | 61.00% | 3.80% | 26.18% | 8.98% | NA |
| Indica Intermediate | 786 | 53.90% | 5.00% | 35.37% | 5.73% | NA |
| Temperate Japonica | 767 | 89.60% | 0.00% | 5.35% | 5.08% | NA |
| Tropical Japonica | 504 | 52.20% | 0.00% | 12.30% | 35.52% | NA |
| Japonica Intermediate | 241 | 51.50% | 0.00% | 15.35% | 33.20% | NA |
| VI/Aromatic | 96 | 26.00% | 0.00% | 20.83% | 53.12% | NA |
| Intermediate | 90 | 75.60% | 0.00% | 15.56% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811932078 | T -> C | LOC_Os08g19920.1 | missense_variant ; p.Val604Ala; MODERATE | nonsynonymous_codon ; V604A | Average:15.841; most accessible tissue: Minghui63 panicle, score: 29.741 | unknown | unknown | TOLERATED | 0.94 |
| vg0811932078 | T -> DEL | LOC_Os08g19920.1 | N | frameshift_variant | Average:15.841; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0811932078 | NA | 3.44E-06 | 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 |
| vg0811932078 | 8.05E-06 | 1.66E-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 |
| vg0811932078 | 2.37E-06 | 7.11E-06 | mr1996_2 | 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 |
| vg0811932078 | 8.53E-06 | NA | mr1996_2 | 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 |