| Variant ID: vg1000993495 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 993495 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TAAGGAGTGCTGTTGGTGCACTTTGTAAACACAGAGAGAAGCAATAAAGTTGTCATCTACTTTGAGAGTTCTTCGATTTGTGTTTCTTCGGGTTCAGGCG[G/T]
CAGGGAGGCGATCTAACCGGCGGCGTGCGAGCGGTCCGACCGGCGGCGACAGGACTACGTCGAGATTTCCATCGATTTGAGGGTAACTTTTATTTCCGCT
AGCGGAAATAAAAGTTACCCTCAAATCGATGGAAATCTCGACGTAGTCCTGTCGCCGCCGGTCGGACCGCTCGCACGCCGCCGGTTAGATCGCCTCCCTG[C/A]
CGCCTGAACCCGAAGAAACACAAATCGAAGAACTCTCAAAGTAGATGACAACTTTATTGCTTCTCTCTGTGTTTACAAAGTGCACCAACAGCACTCCTTA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.70% | 0.60% | 1.97% | 24.69% | NA |
| All Indica | 2759 | 59.30% | 1.10% | 3.19% | 36.46% | NA |
| All Japonica | 1512 | 93.00% | 0.00% | 0.20% | 6.81% | NA |
| Aus | 269 | 83.60% | 0.00% | 0.37% | 15.99% | NA |
| Indica I | 595 | 46.60% | 0.00% | 3.87% | 49.58% | NA |
| Indica II | 465 | 54.00% | 0.40% | 2.37% | 43.23% | NA |
| Indica III | 913 | 67.30% | 2.40% | 3.29% | 27.05% | NA |
| Indica Intermediate | 786 | 62.70% | 0.80% | 3.05% | 33.46% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.00% | 1.69% | NA |
| Tropical Japonica | 504 | 87.30% | 0.00% | 0.60% | 12.10% | NA |
| Japonica Intermediate | 241 | 88.00% | 0.00% | 0.00% | 12.03% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 1.11% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000993495 | G -> T | LOC_Os10g02600.1 | synonymous_variant ; p.Arg117Arg; LOW | synonymous_codon | Average:23.416; most accessible tissue: Callus, score: 40.107 | N | N | N | N |
| vg1000993495 | G -> DEL | LOC_Os10g02600.1 | N | frameshift_variant | Average:23.416; most accessible tissue: Callus, score: 40.107 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000993495 | NA | 4.13E-06 | mr1140 | 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 |
| vg1000993495 | 5.14E-07 | 7.53E-07 | mr1203 | 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 |
| vg1000993495 | 2.50E-06 | 2.53E-06 | mr1618 | 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 |
| vg1000993495 | 8.31E-06 | 8.31E-06 | mr1852 | 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 |