| Variant ID: vg0602313316 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 2313316 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCGTCAGTGTCAGTATCTACTCCTTCCGTCTCATAAAAAACTAAATTAGTACTGGATGTGACACATCCTGGTTAGGGGTGAAAACGGTATGGAAACGGAC[G/A]
GAATCCATCTTTATCGTTTTCGTTTTCATATTTTTTTTCGGAATCGGAAACCCCGAATACGAAAACGGAATCGAATATTATCTAAACCGAAAACGGAGCG
CGCTCCGTTTTCGGTTTAGATAATATTCGATTCCGTTTTCGTATTCGGGGTTTCCGATTCCGAAAAAAAATATGAAAACGAAAACGATAAAGATGGATTC[C/T]
GTCCGTTTCCATACCGTTTTCACCCCTAACCAGGATGTGTCACATCCAGTACTAATTTAGTTTTTTATGAGACGGAAGGAGTAGATACTGACACTGACGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.30% | 1.70% | 1.08% | 1.97% | NA |
| All Indica | 2759 | 99.20% | 0.20% | 0.14% | 0.47% | NA |
| All Japonica | 1512 | 92.90% | 4.40% | 2.65% | 0.07% | NA |
| Aus | 269 | 68.80% | 0.00% | 2.23% | 29.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.40% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.00% | 0.11% | 0.33% | NA |
| Indica Intermediate | 786 | 98.00% | 0.50% | 0.25% | 1.27% | NA |
| Temperate Japonica | 767 | 88.00% | 8.10% | 3.78% | 0.13% | NA |
| Tropical Japonica | 504 | 98.60% | 0.00% | 1.39% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 2.10% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602313316 | G -> A | LOC_Os06g05160-LOC_Os06g05180 | intergenic_region ; MODIFIER | silent_mutation | Average:82.668; most accessible tissue: Minghui63 young leaf, score: 91.049 | N | N | N | N |
| vg0602313316 | G -> DEL | N | N | silent_mutation | Average:82.668; most accessible tissue: Minghui63 young leaf, score: 91.049 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0602313316 | NA | 5.67E-06 | mr1026 | 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 |
| vg0602313316 | NA | 1.87E-10 | mr1712 | 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 |
| vg0602313316 | 9.35E-07 | 9.35E-07 | mr1770 | 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 |
| vg0602313316 | 1.43E-10 | 1.43E-10 | mr1910 | 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 |
| vg0602313316 | 1.45E-06 | 1.92E-08 | mr1161_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 |