| Variant ID: vg0804915302 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4915302 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TATGAAGAAAATTAATGATGACTTAGCTTTGTAATATTCCCCTTGGTGATGGCAGAGGTGGCCAATGTGGGAACAAAGTCGTCCATCAATAACAATGAAG[A/G]
CACCAGTCGGCGACGACGAAGGCGGTCGACGGTGAAAGCGAAGATGCTCACCAACGACGGCATAATAGGCCGGCCGTGTTGGCAGAGACACCAGTCGGCA
TGCCGACTGGTGTCTCTGCCAACACGGCCGGCCTATTATGCCGTCGTTGGTGAGCATCTTCGCTTTCACCGTCGACCGCCTTCGTCGTCGCCGACTGGTG[T/C]
CTTCATTGTTATTGATGGACGACTTTGTTCCCACATTGGCCACCTCTGCCATCACCAAGGGGAATATTACAAAGCTAAGTCATCATTAATTTTCTTCATA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.90% | 8.80% | 4.72% | 21.54% | NA |
| All Indica | 2759 | 63.30% | 14.60% | 4.89% | 17.22% | NA |
| All Japonica | 1512 | 71.60% | 0.10% | 3.70% | 24.54% | NA |
| Aus | 269 | 48.00% | 0.40% | 8.55% | 43.12% | NA |
| Indica I | 595 | 91.90% | 2.90% | 0.67% | 4.54% | NA |
| Indica II | 465 | 54.00% | 7.50% | 4.30% | 34.19% | NA |
| Indica III | 913 | 50.70% | 26.30% | 8.11% | 14.90% | NA |
| Indica Intermediate | 786 | 61.80% | 14.00% | 4.71% | 19.47% | NA |
| Temperate Japonica | 767 | 90.40% | 0.00% | 0.65% | 9.00% | NA |
| Tropical Japonica | 504 | 43.50% | 0.40% | 8.53% | 47.62% | NA |
| Japonica Intermediate | 241 | 71.00% | 0.00% | 3.32% | 25.73% | NA |
| VI/Aromatic | 96 | 44.80% | 3.10% | 6.25% | 45.83% | NA |
| Intermediate | 90 | 73.30% | 10.00% | 3.33% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804915302 | A -> G | LOC_Os08g08530.1 | missense_variant ; p.Ser339Pro; MODERATE | nonsynonymous_codon ; S339P | Average:41.094; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0804915302 | A -> DEL | LOC_Os08g08530.1 | N | frameshift_variant | Average:41.094; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0804915302 | 2.22E-06 | NA | mr1281 | 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 |
| vg0804915302 | NA | 8.06E-07 | mr1281 | 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 |
| vg0804915302 | 7.08E-08 | 7.08E-08 | mr1281_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 |
| vg0804915302 | NA | 9.16E-06 | mr1671_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 |