| Variant ID: vg1004191692 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4191692 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGGGGTTCTTCATCAGGGCGAGTGCGGACTGATTGTCCACCCTCAACTCGACAACCTCAGCTGCAGCACCTCTGAGATCGCCAAGGAGCCGGGCAAGCCA[T/A]
ATGCCCTGGCACGCAGCCGATGCAGCCGCGATGTACTCAGCTTCACAGGAGGAAAGCGCCACAACTTTCTACTTCTGAGATTGCCACCTAACAGGATTGT
ACAATCCTGTTAGGTGGCAATCTCAGAAGTAGAAAGTTGTGGCGCTTTCCTCCTGTGAAGCTGAGTACATCGCGGCTGCATCGGCTGCGTGCCAGGGCAT[A/T]
TGGCTTGCCCGGCTCCTTGGCGATCTCAGAGGTGCTGCAGCTGAGGTTGTCGAGTTGAGGGTGGACAATCAGTCCGCACTCGCCCTGATGAAGAACCCCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.80% | 6.50% | 4.38% | 23.30% | NA |
| All Indica | 2759 | 62.10% | 5.90% | 4.31% | 27.73% | NA |
| All Japonica | 1512 | 84.30% | 4.00% | 2.71% | 8.99% | NA |
| Aus | 269 | 11.20% | 23.80% | 9.67% | 55.39% | NA |
| Indica I | 595 | 60.70% | 2.50% | 3.36% | 33.45% | NA |
| Indica II | 465 | 54.40% | 4.90% | 4.09% | 36.56% | NA |
| Indica III | 913 | 61.30% | 9.50% | 6.24% | 22.89% | NA |
| Indica Intermediate | 786 | 68.40% | 4.80% | 2.93% | 23.79% | NA |
| Temperate Japonica | 767 | 94.00% | 1.00% | 0.78% | 4.17% | NA |
| Tropical Japonica | 504 | 79.00% | 6.50% | 4.56% | 9.92% | NA |
| Japonica Intermediate | 241 | 64.30% | 8.30% | 4.98% | 22.41% | NA |
| VI/Aromatic | 96 | 35.40% | 17.70% | 11.46% | 35.42% | NA |
| Intermediate | 90 | 66.70% | 3.30% | 11.11% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1004191692 | T -> A | LOC_Os10g07578.1 | synonymous_variant ; p.Ile1123Ile; LOW | synonymous_codon | Average:14.394; most accessible tissue: Callus, score: 76.668 | N | N | N | N |
| vg1004191692 | T -> DEL | LOC_Os10g07578.1 | N | frameshift_variant | Average:14.394; most accessible tissue: Callus, score: 76.668 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004191692 | NA | 1.75E-15 | mr1156 | 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 |
| vg1004191692 | NA | 7.90E-06 | mr1295 | 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 |
| vg1004191692 | 7.79E-07 | 9.52E-07 | mr1489 | 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 |
| vg1004191692 | 1.70E-06 | NA | mr1491 | 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 |
| vg1004191692 | 9.84E-06 | 2.62E-17 | mr1768 | 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 |
| vg1004191692 | NA | 1.34E-07 | mr1696_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 |