| Variant ID: vg0706440810 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 6440810 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GAAGGTTTCCTATGTGGATTAGGACTTCTAGTATGAGTTTGGTTCGTGGCTTTAGGCTTCCTACCTCATGTATAAATTGAGAGGGAGCGTGAGGCTTCCC[G/A]
GTATCACTTTTGAGAGCATTGAGTTGATATTTTAGTTAGGTGTTCGAGTTTAGTCGAGATTTTTATAAAGAGTGTTGTTGTTGCACTTTGTAAATGCGAA
TTCGCATTTACAAAGTGCAACAACAACACTCTTTATAAAAATCTCGACTAAACTCGAACACCTAACTAAAATATCAACTCAATGCTCTCAAAAGTGATAC[C/T]
GGGAAGCCTCACGCTCCCTCTCAATTTATACATGAGGTAGGAAGCCTAAAGCCACGAACCAAACTCATACTAGAAGTCCTAATCCACATAGGAAACCTTC
| 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 | 80.60% | 7.00% | 2.18% | 10.20% | NA |
| All Indica | 2759 | 84.10% | 1.10% | 2.03% | 12.83% | NA |
| All Japonica | 1512 | 86.70% | 13.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 35.70% | 3.00% | 16.73% | 44.61% | NA |
| Indica I | 595 | 87.10% | 0.00% | 1.85% | 11.09% | NA |
| Indica II | 465 | 96.30% | 0.40% | 1.08% | 2.15% | NA |
| Indica III | 913 | 80.50% | 0.70% | 1.86% | 16.98% | NA |
| Indica Intermediate | 786 | 78.80% | 2.70% | 2.93% | 15.65% | NA |
| Temperate Japonica | 767 | 93.40% | 6.50% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 90.30% | 9.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 58.10% | 41.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 10.40% | 87.50% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 78.90% | 13.30% | 0.00% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0706440810 | G -> DEL | N | N | silent_mutation | Average:37.27; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg0706440810 | G -> A | LOC_Os07g11650-LOC_Os07g11670 | intergenic_region ; MODIFIER | silent_mutation | Average:37.27; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0706440810 | 4.50E-06 | NA | mr1014 | 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 |
| vg0706440810 | 6.18E-06 | NA | mr1134 | 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 |