| Variant ID: vg1123677787 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 23677787 |
| Reference Allele: GAGGAGCTCCTTCGAT | Alternative Allele: G |
| Primary Allele: GAGGAGCTCCTTCGAT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAATGGTCTTCCCCGTACCACGTAGCCCTAGGATGGAGATGACATTCGGCTCTCGGTGTTGGAGGAAATGGACATATTGGTCCATCAACGGAATCCGGTC[GAGGAGCTCCTTCGAT/G]
ACTTCCGTTAATAGGTCGGAGTCGTCGTCGGCCAATATGCGCCGCCTCTCGAGGTCTTCATGCTCGGATGCGGCACGCTGATGCTGCTGCTCGCGTGCAG
CTGCACGCGAGCAGCAGCATCAGCGTGCCGCATCCGAGCATGAAGACCTCGAGAGGCGGCGCATATTGGCCGACGACGACTCCGACCTATTAACGGAAGT[ATCGAAGGAGCTCCTC/C]
GACCGGATTCCGTTGATGGACCAATATGTCCATTTCCTCCAACACCGAGAGCCGAATGTCATCTCCATCCTAGGGCTACGTGGTACGGGGAAGACCATTC
| Populations | Population Size | Frequency of GAGGAGCTCCTTCGAT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.20% | 2.10% | 0.42% | 6.31% | NA |
| All Indica | 2759 | 89.60% | 0.40% | 0.58% | 9.39% | NA |
| All Japonica | 1512 | 96.50% | 2.50% | 0.20% | 0.79% | NA |
| Aus | 269 | 79.90% | 17.50% | 0.37% | 2.23% | NA |
| Indica I | 595 | 95.00% | 0.20% | 0.17% | 4.71% | NA |
| Indica II | 465 | 79.80% | 0.40% | 0.43% | 19.35% | NA |
| Indica III | 913 | 89.20% | 0.10% | 0.99% | 9.75% | NA |
| Indica Intermediate | 786 | 91.90% | 1.00% | 0.51% | 6.62% | NA |
| Temperate Japonica | 767 | 96.30% | 2.20% | 0.13% | 1.30% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 90.90% | 7.50% | 0.83% | 0.83% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 0.00% | 15.62% | NA |
| Intermediate | 90 | 92.20% | 1.10% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1123677787 | GAGGAGCTCCTTCGAT -> DEL | LOC_Os11g39730.1 | N | frameshift_variant | Average:48.092; most accessible tissue: Zhenshan97 panicle, score: 84.374 | N | N | N | N |
| vg1123677787 | GAGGAGCTCCTTCGAT -> G | LOC_Os11g39730.1 | disruptive_inframe_deletion ; p.Ser194_Leu198del; MODERATE | inframe_variant | Average:48.092; most accessible tissue: Zhenshan97 panicle, score: 84.374 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1123677787 | 2.34E-06 | 1.47E-07 | mr1238 | 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 |
| vg1123677787 | 2.90E-06 | 1.73E-07 | mr1309 | 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 |
| vg1123677787 | 6.93E-07 | 6.92E-07 | mr1566 | 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 |
| vg1123677787 | 9.60E-06 | 5.98E-08 | mr1841 | 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 |