| Variant ID: vg1205810377 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 5810377 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTCCTAACCTCCTCCTATTTGAAAATTTGTGTAAATAGAGGTAAGTGCATGAAAGTAGTGATTAGTGGTACCCAAAAAAAAAGATACTTACGACGAAATC[A/G]
TCGTCGTCAATGTTAGGACACACGAAGCATCTTTGTCCTCGAGTTCGTTGTCTTACGGACCTTATCACCTGACAACGGTCACCACAACGACACTCTGGAT
ATCCAGAGTGTCGTTGTGGTGACCGTTGTCAGGTGATAAGGTCCGTAAGACAACGAACTCGAGGACAAAGATGCTTCGTGTGTCCTAACATTGACGACGA[T/C]
GATTTCGTCGTAAGTATCTTTTTTTTTGGGTACCACTAATCACTACTTTCATGCACTTACCTCTATTTACACAAATTTTCAAATAGGAGGAGGTTAGGAA
| 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 | 66.90% | 17.30% | 11.43% | 4.38% | NA |
| All Indica | 2759 | 52.90% | 29.20% | 16.35% | 1.56% | NA |
| All Japonica | 1512 | 94.50% | 0.20% | 0.86% | 4.43% | NA |
| Aus | 269 | 68.00% | 0.00% | 21.56% | 10.41% | NA |
| Indica I | 595 | 93.30% | 2.70% | 1.68% | 2.35% | NA |
| Indica II | 465 | 29.00% | 50.50% | 19.14% | 1.29% | NA |
| Indica III | 913 | 37.00% | 39.90% | 22.89% | 0.22% | NA |
| Indica Intermediate | 786 | 54.80% | 24.30% | 18.19% | 2.67% | NA |
| Temperate Japonica | 767 | 90.90% | 0.10% | 0.52% | 8.47% | NA |
| Tropical Japonica | 504 | 98.20% | 0.20% | 1.39% | 0.20% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.40% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 30.20% | 2.10% | 8.33% | 59.38% | NA |
| Intermediate | 90 | 67.80% | 7.80% | 11.11% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1205810377 | A -> DEL | N | N | silent_mutation | Average:19.997; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |
| vg1205810377 | A -> G | LOC_Os12g10784.1 | downstream_gene_variant ; 3139.0bp to feature; MODIFIER | silent_mutation | Average:19.997; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |
| vg1205810377 | A -> G | LOC_Os12g10784.2 | downstream_gene_variant ; 3139.0bp to feature; MODIFIER | silent_mutation | Average:19.997; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |
| vg1205810377 | A -> G | LOC_Os12g10784.3 | downstream_gene_variant ; 3139.0bp to feature; MODIFIER | silent_mutation | Average:19.997; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |
| vg1205810377 | A -> G | LOC_Os12g10800.1 | intron_variant ; MODIFIER | silent_mutation | Average:19.997; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1205810377 | NA | 4.93E-06 | mr1749 | 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 |
| vg1205810377 | NA | 6.93E-08 | mr1757 | 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 |
| vg1205810377 | NA | 4.15E-11 | mr1565_2 | 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 |