| Variant ID: vg0417381371 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17381371 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 66. )
TTCCAAGGCACCAAGGAAGAGGTTAGATTTAGATATCACCTTTCATTTATATGCCACATACTTTTGTTTTGTCAGTGGTATGCCAACAGATAGATTGCAA[C/T]
AGGACACGGTCTTCTCCAGGAAGTGCTACGGTCAAAAAACTTTTCAAGGAAGATGATGAGCAAAAGGGTGAAAAGTGGTATTCCTCTTCCCCTTCACACG
CGTGTGAAGGGGAAGAGGAATACCACTTTTCACCCTTTTGCTCATCATCTTCCTTGAAAAGTTTTTTGACCGTAGCACTTCCTGGAGAAGACCGTGTCCT[G/A]
TTGCAATCTATCTGTTGGCATACCACTGACAAAACAAAAGTATGTGGCATATAAATGAAAGGTGATATCTAAATCTAACCTCTTCCTTGGTGCCTTGGAA
| 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 | 46.00% | 43.30% | 4.02% | 6.71% | NA |
| All Indica | 2759 | 20.70% | 71.80% | 4.57% | 2.94% | NA |
| All Japonica | 1512 | 81.50% | 0.70% | 3.17% | 14.62% | NA |
| Aus | 269 | 91.10% | 5.60% | 1.49% | 1.86% | NA |
| Indica I | 595 | 23.50% | 54.50% | 10.76% | 11.26% | NA |
| Indica II | 465 | 42.80% | 53.50% | 3.44% | 0.22% | NA |
| Indica III | 913 | 4.70% | 94.40% | 0.44% | 0.44% | NA |
| Indica Intermediate | 786 | 24.00% | 69.50% | 5.34% | 1.15% | NA |
| Temperate Japonica | 767 | 70.10% | 0.30% | 4.56% | 25.03% | NA |
| Tropical Japonica | 504 | 97.60% | 1.20% | 0.99% | 0.20% | NA |
| Japonica Intermediate | 241 | 83.80% | 1.20% | 3.32% | 11.62% | NA |
| VI/Aromatic | 96 | 64.60% | 22.90% | 5.21% | 7.29% | NA |
| Intermediate | 90 | 68.90% | 20.00% | 7.78% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0417381371 | C -> DEL | N | N | silent_mutation | Average:28.661; most accessible tissue: Minghui63 flag leaf, score: 41.254 | N | N | N | N |
| vg0417381371 | C -> T | LOC_Os04g29310.1 | intron_variant ; MODIFIER | silent_mutation | Average:28.661; most accessible tissue: Minghui63 flag leaf, score: 41.254 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417381371 | NA | 1.04E-08 | mr1047 | 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 |
| vg0417381371 | NA | 7.49E-06 | mr1189 | 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 |
| vg0417381371 | NA | 3.39E-06 | mr1625 | 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 |
| vg0417381371 | 1.72E-06 | 7.71E-08 | mr1864 | 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 |
| vg0417381371 | NA | 5.25E-06 | mr1677_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 |