| Variant ID: vg1000738566 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 738566 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCGTAGCTTTCTTGACGTCATGATTACGGCGTAGAGCAGTTTTTGGATCTGTTGGTATCTTGTCTATGCGTCGTGTAGAGCTTCGCTGACGTAATAGACT[G/A]
GTCTCTGCACCTTTTCTCTTTCGAAAATAATGACAGTACTCACAGAGTAGGGCATGGCGGCGATATAGAGGAACAACACTTCATTAAGTTGGGGAGCAAC
GTTGCTCCCCAACTTAATGAAGTGTTGTTCCTCTATATCGCCGCCATGCCCTACTCTGTGAGTACTGTCATTATTTTCGAAAGAGAAAAGGTGCAGAGAC[C/T]
AGTCTATTACGTCAGCGAAGCTCTACACGACGCATAGACAAGATACCAACAGATCCAAAAACTGCTCTACGCCGTAATCATGACGTCAAGAAAGCTACGC
| 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 | 58.30% | 2.50% | 2.35% | 36.92% | NA |
| All Indica | 2759 | 55.50% | 0.90% | 2.25% | 41.43% | NA |
| All Japonica | 1512 | 53.20% | 6.10% | 3.04% | 37.70% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 67.20% | 0.00% | 2.35% | 30.42% | NA |
| Indica II | 465 | 29.20% | 0.40% | 3.87% | 66.45% | NA |
| Indica III | 913 | 54.40% | 2.00% | 1.86% | 41.73% | NA |
| Indica Intermediate | 786 | 63.20% | 0.50% | 1.65% | 34.61% | NA |
| Temperate Japonica | 767 | 79.10% | 9.50% | 1.83% | 9.52% | NA |
| Tropical Japonica | 504 | 11.90% | 2.60% | 2.98% | 82.54% | NA |
| Japonica Intermediate | 241 | 56.80% | 2.50% | 7.05% | 33.61% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 1.10% | 3.33% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000738566 | G -> A | LOC_Os10g02150.1 | downstream_gene_variant ; 2650.0bp to feature; MODIFIER | silent_mutation | Average:19.951; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 | N | N | N | N |
| vg1000738566 | G -> A | LOC_Os10g02170.1 | downstream_gene_variant ; 1091.0bp to feature; MODIFIER | silent_mutation | Average:19.951; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 | N | N | N | N |
| vg1000738566 | G -> A | LOC_Os10g02160.1 | intron_variant ; MODIFIER | silent_mutation | Average:19.951; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 | N | N | N | N |
| vg1000738566 | G -> DEL | N | N | silent_mutation | Average:19.951; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000738566 | 1.89E-09 | NA | mr1310_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 |
| vg1000738566 | NA | 1.12E-06 | mr1549_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 |
| vg1000738566 | NA | 3.04E-06 | mr1757_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 |
| vg1000738566 | 9.70E-07 | NA | mr1959_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 |