| Variant ID: vg0402179892 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2179892 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCGGCGGTGGAGCATTGTTGTTCCCTTGGTTGAGCTGGTTCTGCTGGTTCTGGAGTTGCTGCATCATCATGTTCATAAGCTGTGTCTGTTGAGCCAGAAC[C/T]
TGGGCAAGTGTGGGATTCTCTCCATTGTTGTTGTTATTGTTATTGTTGGGGCCATTCCCGTTGCTGCGAGTGAGCACCATCTGGCAGGGACAAGAGCACA
TGTGCTCTTGTCCCTGCCAGATGGTGCTCACTCGCAGCAACGGGAATGGCCCCAACAATAACAATAACAACAACAATGGAGAGAATCCCACACTTGCCCA[G/A]
GTTCTGGCTCAACAGACACAGCTTATGAACATGATGATGCAGCAACTCCAGAACCAGCAGAACCAGCTCAACCAAGGGAACAACAATGCTCCACCGCCGC
| 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 | 50.40% | 1.10% | 12.23% | 36.25% | NA |
| All Indica | 2759 | 45.80% | 0.60% | 11.74% | 41.90% | NA |
| All Japonica | 1512 | 64.70% | 2.20% | 8.73% | 24.34% | NA |
| Aus | 269 | 18.60% | 0.00% | 36.43% | 44.98% | NA |
| Indica I | 595 | 52.30% | 0.20% | 9.58% | 37.98% | NA |
| Indica II | 465 | 42.20% | 0.60% | 15.27% | 41.94% | NA |
| Indica III | 913 | 46.70% | 0.70% | 12.49% | 40.20% | NA |
| Indica Intermediate | 786 | 42.00% | 0.80% | 10.43% | 46.82% | NA |
| Temperate Japonica | 767 | 85.10% | 0.00% | 0.65% | 14.21% | NA |
| Tropical Japonica | 504 | 38.70% | 3.20% | 22.62% | 35.52% | NA |
| Japonica Intermediate | 241 | 54.40% | 7.10% | 5.39% | 33.20% | NA |
| VI/Aromatic | 96 | 44.80% | 1.00% | 7.29% | 46.88% | NA |
| Intermediate | 90 | 52.20% | 3.30% | 18.89% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402179892 | C -> DEL | LOC_Os04g04550.1 | N | frameshift_variant | Average:7.31; most accessible tissue: Zhenshan97 young leaf, score: 14.714 | N | N | N | N |
| vg0402179892 | C -> T | LOC_Os04g04550.1 | synonymous_variant ; p.Gln27Gln; LOW | synonymous_codon | Average:7.31; most accessible tissue: Zhenshan97 young leaf, score: 14.714 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402179892 | NA | 1.81E-06 | mr1252 | 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 |
| vg0402179892 | NA | 1.50E-06 | mr1291 | 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 |
| vg0402179892 | NA | 9.21E-08 | mr1599_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 |
| vg0402179892 | 4.81E-06 | 4.00E-07 | mr1781_2 | Jap_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 |