| Variant ID: vg0817496643 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17496643 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATCTCATGGCAGATGAGAGGGAGGATTTGGTTCAGTCAAGATTGCGAGCTCTTGCAAAAGTTACCAACGACAAAGAAAGGGTTGCTCGACATTATAACAA[G/A]
AAGGTAGTGCCTAAGTCTTTTTCTGAGGGAGAGCTTTTTTGGAAGTTAATCTTGCTGATAGGAACTCGAGATAACAAATTCGGCAAGTGGTCACCAAACT
AGTTTGGTGACCACTTGCCGAATTTGTTATCTCGAGTTCCTATCAGCAAGATTAACTTCCAAAAAAGCTCTCCCTCAGAAAAAGACTTAGGCACTACCTT[C/T]
TTGTTATAATGTCGAGCAACCCTTTCTTTGTCGTTGGTAACTTTTGCAAGAGCTCGCAATCTTGACTGAACCAAATCCTCCCTCTCATCTGCCATGAGAT
| 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 | 68.70% | 10.50% | 13.99% | 6.77% | NA |
| All Indica | 2759 | 57.20% | 12.10% | 20.62% | 10.11% | NA |
| All Japonica | 1512 | 86.80% | 9.10% | 2.78% | 1.26% | NA |
| Aus | 269 | 75.80% | 3.00% | 16.36% | 4.83% | NA |
| Indica I | 595 | 82.20% | 1.30% | 13.28% | 3.19% | NA |
| Indica II | 465 | 53.50% | 4.70% | 12.47% | 29.25% | NA |
| Indica III | 913 | 45.10% | 24.60% | 26.29% | 3.94% | NA |
| Indica Intermediate | 786 | 54.30% | 10.10% | 24.43% | 11.20% | NA |
| Temperate Japonica | 767 | 98.80% | 0.40% | 0.26% | 0.52% | NA |
| Tropical Japonica | 504 | 66.50% | 24.00% | 6.94% | 2.58% | NA |
| Japonica Intermediate | 241 | 91.30% | 5.80% | 2.07% | 0.83% | NA |
| VI/Aromatic | 96 | 89.60% | 6.20% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 75.60% | 12.20% | 3.33% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817496643 | G -> A | LOC_Os08g28630.1 | synonymous_variant ; p.Lys1435Lys; LOW | synonymous_codon | Average:11.023; most accessible tissue: Callus, score: 33.447 | N | N | N | N |
| vg0817496643 | G -> DEL | LOC_Os08g28630.1 | N | frameshift_variant | Average:11.023; most accessible tissue: Callus, score: 33.447 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817496643 | NA | 6.58E-06 | mr1594_2 | Ind_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 |
| vg0817496643 | 3.89E-06 | 9.19E-06 | mr1916_2 | 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 |