| Variant ID: vg0710897646 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10897646 |
| Reference Allele: C | Alternative Allele: T,G |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGGCAACTGTGCTATCTTCGTCGTTTGCCTCTTTCACCGATGGCTTTGTCAGGACGTCCAGAGAGGTGCCGGGTTTGAGTGGCTCCCGTCTGGACGCACG[C/T,G]
CGTGCTAGATCATCTGGTTCGATGTTGTCCTTGCGGTATACGTGTCGGACCTCGATTCCATCAAATCTTTTTTCCAGCTTCCTGAGTACTTCTGCGAGGT
ACCTCGCAGAAGTACTCAGGAAGCTGGAAAAAAGATTTGATGGAATCGAGGTCCGACACGTATACCGCAAGGACAACATCGAACCAGATGATCTAGCACG[G/A,C]
CGTGCGTCCAGACGGGAGCCACTCAAACCCGGCACCTCTCTGGACGTCCTGACAAAGCCATCGGTGAAAGAGGCAAACGACGAAGATAGCACAGTTGCCC
| 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 | 82.30% | 6.90% | 2.73% | 7.89% | G: 0.17% |
| All Indica | 2759 | 75.10% | 11.70% | 4.39% | 8.70% | G: 0.18% |
| All Japonica | 1512 | 91.70% | 0.10% | 0.13% | 8.13% | NA |
| Aus | 269 | 98.10% | 0.00% | 1.49% | 0.37% | NA |
| Indica I | 595 | 66.40% | 18.30% | 10.42% | 4.87% | NA |
| Indica II | 465 | 74.60% | 8.60% | 2.37% | 14.41% | NA |
| Indica III | 913 | 82.40% | 6.80% | 1.75% | 8.65% | G: 0.44% |
| Indica Intermediate | 786 | 73.40% | 14.10% | 4.07% | 8.27% | G: 0.13% |
| Temperate Japonica | 767 | 84.70% | 0.10% | 0.26% | 14.86% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 6.25% | G: 2.08% |
| Intermediate | 90 | 91.10% | 2.20% | 2.22% | 3.33% | G: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710897646 | C -> DEL | N | N | silent_mutation | Average:17.915; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0710897646 | C -> G | LOC_Os07g18390.1 | downstream_gene_variant ; 1966.0bp to feature; MODIFIER | silent_mutation | Average:17.915; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0710897646 | C -> G | LOC_Os07g18410.1 | downstream_gene_variant ; 1128.0bp to feature; MODIFIER | silent_mutation | Average:17.915; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0710897646 | C -> G | LOC_Os07g18420.1 | downstream_gene_variant ; 3885.0bp to feature; MODIFIER | silent_mutation | Average:17.915; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0710897646 | C -> G | LOC_Os07g18400.1 | intron_variant ; MODIFIER | silent_mutation | Average:17.915; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0710897646 | C -> T | LOC_Os07g18390.1 | downstream_gene_variant ; 1966.0bp to feature; MODIFIER | silent_mutation | Average:17.915; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0710897646 | C -> T | LOC_Os07g18410.1 | downstream_gene_variant ; 1128.0bp to feature; MODIFIER | silent_mutation | Average:17.915; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0710897646 | C -> T | LOC_Os07g18420.1 | downstream_gene_variant ; 3885.0bp to feature; MODIFIER | silent_mutation | Average:17.915; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0710897646 | C -> T | LOC_Os07g18400.1 | intron_variant ; MODIFIER | silent_mutation | Average:17.915; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0710897646 | NA | 6.07E-14 | mr1026 | 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 |
| vg0710897646 | NA | 6.64E-15 | mr1118 | 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 |
| vg0710897646 | NA | 2.32E-15 | mr1118 | 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 |
| vg0710897646 | NA | 1.67E-13 | mr1161 | 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 |
| vg0710897646 | 5.06E-06 | NA | mr1495 | 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 |
| vg0710897646 | 8.01E-07 | 9.84E-18 | mr1495 | 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 |
| vg0710897646 | NA | 2.05E-08 | mr1496 | 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 |
| vg0710897646 | NA | 2.99E-13 | mr1118_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 |
| vg0710897646 | NA | 2.26E-11 | mr1161_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 |
| vg0710897646 | NA | 5.26E-13 | mr1495_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 |