| Variant ID: vg0716176808 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 16176808 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 85. )
ATCAGCTAAAGTGATCGTCGGCTCAGTAGTTGGGGCAGGTGGACCATGGTGGTTACTGCAAACTTGGCTGAACTTGGTAGTCATGAAAGTTGTCAATCGG[T/C]
CATTTGTGATAGAAGCCGAATTTCCAAGGTTGGAGCCGATCATGGAAGATGATGGAGAAGAACACACTCATCGTAGATGCATGTCATACGGAGAATATGC
GCATATTCTCCGTATGACATGCATCTACGATGAGTGTGTTCTTCTCCATCATCTTCCATGATCGGCTCCAACCTTGGAAATTCGGCTTCTATCACAAATG[A/G]
CCGATTGACAACTTTCATGACTACCAAGTTCAGCCAAGTTTGCAGTAACCACCATGGTCCACCTGCCCCAACTACTGAGCCGACGATCACTTTAGCTGAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.10% | 37.60% | 7.77% | 11.55% | NA |
| All Indica | 2759 | 69.30% | 5.30% | 11.63% | 13.77% | NA |
| All Japonica | 1512 | 2.40% | 97.20% | 0.13% | 0.26% | NA |
| Aus | 269 | 23.40% | 9.70% | 13.38% | 53.53% | NA |
| Indica I | 595 | 59.20% | 3.90% | 17.48% | 19.50% | NA |
| Indica II | 465 | 75.50% | 5.40% | 5.38% | 13.76% | NA |
| Indica III | 913 | 78.20% | 1.60% | 8.98% | 11.17% | NA |
| Indica Intermediate | 786 | 63.10% | 10.40% | 13.99% | 12.47% | NA |
| Temperate Japonica | 767 | 4.30% | 95.30% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 98.30% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 6.20% | 90.60% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 22.20% | 52.20% | 7.78% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0716176808 | T -> DEL | N | N | silent_mutation | Average:10.614; most accessible tissue: Callus, score: 40.755 | N | N | N | N |
| vg0716176808 | T -> C | LOC_Os07g27740.1 | downstream_gene_variant ; 2839.0bp to feature; MODIFIER | silent_mutation | Average:10.614; most accessible tissue: Callus, score: 40.755 | N | N | N | N |
| vg0716176808 | T -> C | LOC_Os07g27730.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.614; most accessible tissue: Callus, score: 40.755 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0716176808 | 7.32E-08 | NA | mr1004 | 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 |
| vg0716176808 | NA | 4.45E-09 | mr1005 | 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 |
| vg0716176808 | 3.04E-07 | NA | mr1005 | 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 |
| vg0716176808 | 7.61E-06 | 7.35E-06 | mr1265_2 | 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 |
| vg0716176808 | NA | 2.64E-06 | mr1754_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 |