| Variant ID: vg0802884967 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 2884967 |
| Reference Allele: C | Alternative Allele: G,T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CACTACCCACTTGTCAGCGTTATCCCTGTCACTATTCTAGTGCACCACTGGTTCCTAGCTACAAGACCGTCGTGCCCACACATTATCCAAAAGCACATGC[C/G,T]
AATGCATAGGCTAATGAATAATTAATTGCAATATCTCACTTTTAATGCATGTTTATCTCTCTTATCTAGATTTTCTTCGGCACTAAAAATTATTGCTCCT
AGGAGCAATAATTTTTAGTGCCGAAGAAAATCTAGATAAGAGAGATAAACATGCATTAAAAGTGAGATATTGCAATTAATTATTCATTAGCCTATGCATT[G/C,A]
GCATGTGCTTTTGGATAATGTGTGGGCACGACGGTCTTGTAGCTAGGAACCAGTGGTGCACTAGAATAGTGACAGGGATAACGCTGACAAGTGGGTAGTG
| 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 | 38.70% | 17.50% | 6.39% | 32.65% | G: 4.80% |
| All Indica | 2759 | 11.50% | 29.40% | 7.72% | 43.39% | G: 8.01% |
| All Japonica | 1512 | 78.90% | 0.20% | 4.76% | 15.94% | G: 0.20% |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 4.40% | 40.50% | 14.29% | 38.15% | G: 2.69% |
| Indica II | 465 | 11.80% | 19.80% | 7.74% | 58.49% | G: 2.15% |
| Indica III | 913 | 12.60% | 31.70% | 1.64% | 41.07% | G: 13.03% |
| Indica Intermediate | 786 | 15.30% | 24.20% | 9.80% | 41.09% | G: 9.67% |
| Temperate Japonica | 767 | 88.30% | 0.00% | 3.78% | 7.69% | G: 0.26% |
| Tropical Japonica | 504 | 80.00% | 0.40% | 3.17% | 16.27% | G: 0.20% |
| Japonica Intermediate | 241 | 46.90% | 0.40% | 11.20% | 41.49% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 8.33% | 81.25% | G: 1.04% |
| Intermediate | 90 | 50.00% | 7.80% | 10.00% | 30.00% | G: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0802884967 | C -> G | LOC_Os08g05440.1 | intron_variant ; MODIFIER | silent_mutation | Average:45.295; most accessible tissue: Callus, score: 87.617 | N | N | N | N |
| vg0802884967 | C -> T | LOC_Os08g05440.1 | intron_variant ; MODIFIER | silent_mutation | Average:45.295; most accessible tissue: Callus, score: 87.617 | N | N | N | N |
| vg0802884967 | C -> DEL | N | N | silent_mutation | Average:45.295; most accessible tissue: Callus, score: 87.617 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0802884967 | 8.60E-06 | NA | mr1071 | 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 |
| vg0802884967 | NA | 1.99E-07 | mr1321 | 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 |
| vg0802884967 | NA | 1.22E-08 | mr1354 | 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 |
| vg0802884967 | NA | 6.73E-06 | mr1398 | 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 |
| vg0802884967 | 9.11E-07 | NA | mr1618 | 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 |
| vg0802884967 | NA | 4.34E-08 | mr1763 | 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 |
| vg0802884967 | NA | 1.22E-09 | mr1945 | 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 |