| Variant ID: vg1002319935 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 2319935 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTCAAGGGCTGGGGGCGAATAGGTTCCGCCACACCCAGACCCTTCGCCACAATACCAATAAGGTGCGGCGTCAAGGGCTGCGGATGAACAGGTTTCGCCC[G/A,T]
CCCACGCCCTTCGCCATAGTGCTAATAAGGTACGACGTCAAGGGCTGGGGGTGAATAGGTTTTTCCATACCCAAGCCCTTCGCCACAGTACCAATGAGGT
ACCTCATTGGTACTGTGGCGAAGGGCTTGGGTATGGAAAAACCTATTCACCCCCAGCCCTTGACGTCGTACCTTATTAGCACTATGGCGAAGGGCGTGGG[C/T,A]
GGGCGAAACCTGTTCATCCGCAGCCCTTGACGCCGCACCTTATTGGTATTGTGGCGAAGGGTCTGGGTGTGGCGGAACCTATTCGCCCCCAGCCCTTGAC
| 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 | 87.30% | 10.70% | 0.08% | 1.93% | NA |
| All Indica | 2759 | 95.00% | 1.60% | 0.07% | 3.26% | NA |
| All Japonica | 1512 | 69.90% | 30.00% | 0.13% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 82.20% | 5.00% | 0.17% | 12.61% | NA |
| Indica II | 465 | 98.50% | 1.10% | 0.00% | 0.43% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.10% | 1.10% | 0.13% | 1.65% | NA |
| Temperate Japonica | 767 | 59.50% | 40.30% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 50.60% | 49.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 8.90% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1002319935 | G -> T | LOC_Os10g04800.1 | downstream_gene_variant ; 2351.0bp to feature; MODIFIER | N | Average:64.702; most accessible tissue: Minghui63 flag leaf, score: 82.75 | N | N | N | N |
| vg1002319935 | G -> T | LOC_Os10g04810.1 | intron_variant ; MODIFIER | N | Average:64.702; most accessible tissue: Minghui63 flag leaf, score: 82.75 | N | N | N | N |
| vg1002319935 | G -> A | LOC_Os10g04800.1 | downstream_gene_variant ; 2351.0bp to feature; MODIFIER | silent_mutation | Average:64.702; most accessible tissue: Minghui63 flag leaf, score: 82.75 | N | N | N | N |
| vg1002319935 | G -> A | LOC_Os10g04810.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.702; most accessible tissue: Minghui63 flag leaf, score: 82.75 | N | N | N | N |
| vg1002319935 | G -> DEL | N | N | silent_mutation | Average:64.702; most accessible tissue: Minghui63 flag leaf, score: 82.75 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1002319935 | 4.82E-06 | NA | mr1928 | 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 |
| vg1002319935 | NA | 9.22E-08 | mr1709_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 |
| vg1002319935 | NA | 2.23E-06 | mr1768_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 |