| Variant ID: vg0602444850 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 2444850 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTCAGACTCTTTTGGATAAATTTCCTTTAATTGATCCGATTCCACAAAAAACACAACTGCTAGTGACTTGACGACTCCCATCAGCCGATTCCAAGACTCT[G/A]
AAGCCGATACTAACTCTAGGCCAATGATGACTTCGGGCTTACTAAATTTTGGTGTTAACACATGTCTCCCAGTTTTGGAGTATGAGAACTCATGCTTCAA
TTGAAGCATGAGTTCTCATACTCCAAAACTGGGAGACATGTGTTAACACCAAAATTTAGTAAGCCCGAAGTCATCATTGGCCTAGAGTTAGTATCGGCTT[C/T]
AGAGTCTTGGAATCGGCTGATGGGAGTCGTCAAGTCACTAGCAGTTGTGTTTTTTGTGGAATCGGATCAATTAAAGGAAATTTATCCAAAAGAGTCTGAG
| 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 | 42.50% | 1.30% | 4.10% | 52.07% | NA |
| All Indica | 2759 | 18.50% | 0.00% | 4.24% | 77.20% | NA |
| All Japonica | 1512 | 92.30% | 3.60% | 3.51% | 0.53% | NA |
| Aus | 269 | 10.40% | 0.00% | 5.58% | 84.01% | NA |
| Indica I | 595 | 6.90% | 0.00% | 2.86% | 90.25% | NA |
| Indica II | 465 | 50.30% | 0.00% | 3.66% | 46.02% | NA |
| Indica III | 913 | 9.90% | 0.10% | 5.48% | 84.56% | NA |
| Indica Intermediate | 786 | 18.60% | 0.00% | 4.20% | 77.23% | NA |
| Temperate Japonica | 767 | 89.80% | 4.40% | 5.61% | 0.13% | NA |
| Tropical Japonica | 504 | 98.00% | 1.00% | 0.20% | 0.79% | NA |
| Japonica Intermediate | 241 | 88.40% | 6.60% | 3.73% | 1.24% | NA |
| VI/Aromatic | 96 | 19.80% | 3.10% | 4.17% | 72.92% | NA |
| Intermediate | 90 | 61.10% | 3.30% | 5.56% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602444850 | G -> A | LOC_Os06g05410.1 | upstream_gene_variant ; 2313.0bp to feature; MODIFIER | silent_mutation | Average:33.638; most accessible tissue: Minghui63 panicle, score: 64.459 | N | N | N | N |
| vg0602444850 | G -> A | LOC_Os06g05420.1 | downstream_gene_variant ; 4239.0bp to feature; MODIFIER | silent_mutation | Average:33.638; most accessible tissue: Minghui63 panicle, score: 64.459 | N | N | N | N |
| vg0602444850 | G -> A | LOC_Os06g05410-LOC_Os06g05420 | intergenic_region ; MODIFIER | silent_mutation | Average:33.638; most accessible tissue: Minghui63 panicle, score: 64.459 | N | N | N | N |
| vg0602444850 | G -> DEL | N | N | silent_mutation | Average:33.638; most accessible tissue: Minghui63 panicle, score: 64.459 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0602444850 | NA | 9.76E-07 | mr1201 | 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 |
| vg0602444850 | NA | 3.48E-06 | mr1219 | 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 |
| vg0602444850 | 2.93E-06 | 6.40E-07 | mr1201_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 |
| vg0602444850 | NA | 3.68E-06 | mr1219_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 |