| Variant ID: vg0615088196 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 15088196 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTTCATTAACTAGTCGGCGGCGGACGAGGCAGCCGGTCGGTGAGGATGTAGACGCCCAACAACGGCGGCATAATAGGCCAGCCATGCAGGCGGAAACACC[A/T]
GTCGGCGGCGGACGAGGCGACCGGTCGGTGAAGACGTAGACGCTCAACAACAGTGGCATAATAGGCCAGCTGTGCAGGCGGTAACACCAGTCGGTGGCGG
CCGCCACCGACTGGTGTTACCGCCTGCACAGCTGGCCTATTATGCCACTGTTGTTGAGCGTCTACGTCTTCACCGACCGGTCGCCTCGTCCGCCGCCGAC[T/A]
GGTGTTTCCGCCTGCATGGCTGGCCTATTATGCCGCCGTTGTTGGGCGTCTACATCCTCACCGACCGGCTGCCTCGTCCGCCGCCGACTAGTTAATGAAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.00% | 22.50% | 17.01% | 5.46% | NA |
| All Indica | 2759 | 39.50% | 33.50% | 26.57% | 0.47% | NA |
| All Japonica | 1512 | 92.50% | 6.10% | 1.26% | 0.13% | NA |
| Aus | 269 | 8.20% | 14.50% | 10.78% | 66.54% | NA |
| Indica I | 595 | 48.90% | 12.40% | 38.49% | 0.17% | NA |
| Indica II | 465 | 56.60% | 18.10% | 24.95% | 0.43% | NA |
| Indica III | 913 | 21.40% | 58.70% | 19.50% | 0.44% | NA |
| Indica Intermediate | 786 | 43.30% | 29.30% | 26.72% | 0.76% | NA |
| Temperate Japonica | 767 | 97.70% | 1.60% | 0.78% | 0.00% | NA |
| Tropical Japonica | 504 | 83.30% | 14.30% | 2.18% | 0.20% | NA |
| Japonica Intermediate | 241 | 95.40% | 3.30% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 30.20% | 3.10% | 8.33% | 58.33% | NA |
| Intermediate | 90 | 66.70% | 7.80% | 16.67% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0615088196 | A -> T | LOC_Os06g25830.1 | synonymous_variant ; p.Thr158Thr; LOW | synonymous_codon | Average:36.012; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0615088196 | A -> DEL | LOC_Os06g25830.1 | N | frameshift_variant | Average:36.012; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0615088196 | 8.90E-07 | 1.28E-06 | mr1231 | 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 |
| vg0615088196 | 7.25E-06 | 7.25E-06 | mr1412 | 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 |