| Variant ID: vg0417407132 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17407132 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGGAAGATGTGCGCACTGATGAAGAGCGCCAGGAGAGGTTCTTGGAAGGACTTAATGATGAGCTTTCTTACCCACTCATGACTGGGGATTATCATGATTT[C/T]
CTGAAGTTAGTAGATAAGGCTATTCGCCAGGTGGACAAGTACAACCGTATGGAGCAGAAGAAACGCCAGATTGCTCACTTCAAGGCACAACAGGGGAATA
TATTCCCCTGTTGTGCCTTGAAGTGAGCAATCTGGCGTTTCTTCTGCTCCATACGGTTGTACTTGTCCACCTGGCGAATAGCCTTATCTACTAACTTCAG[G/A]
AAATCATGATAATCCCCAGTCATGAGTGGGTAAGAAAGCTCATCATTAAGTCCTTCCAAGAACCTCTCCTGGCGCTCTTCATCAGTGCGCACATCTTCCG
| 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 | 92.90% | 1.50% | 2.58% | 3.00% | NA |
| All Indica | 2759 | 98.30% | 0.10% | 0.98% | 0.62% | NA |
| All Japonica | 1512 | 84.90% | 4.50% | 6.02% | 4.56% | NA |
| Aus | 269 | 79.20% | 0.00% | 0.37% | 20.45% | NA |
| Indica I | 595 | 92.90% | 0.00% | 4.20% | 2.86% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 79.90% | 2.00% | 9.78% | 8.34% | NA |
| Tropical Japonica | 504 | 93.50% | 5.60% | 0.99% | 0.00% | NA |
| Japonica Intermediate | 241 | 83.00% | 10.40% | 4.56% | 2.07% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 3.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0417407132 | C -> DEL | LOC_Os04g29330.1 | N | frameshift_variant | Average:36.523; most accessible tissue: Minghui63 young leaf, score: 60.103 | N | N | N | N |
| vg0417407132 | C -> T | LOC_Os04g29330.1 | synonymous_variant ; p.Phe382Phe; LOW | synonymous_codon | Average:36.523; most accessible tissue: Minghui63 young leaf, score: 60.103 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417407132 | NA | 1.60E-06 | mr1668 | 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 |
| vg0417407132 | 6.25E-06 | NA | mr1291_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 |
| vg0417407132 | 4.97E-07 | NA | mr1993_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 |