| Variant ID: vg0617039640 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 17039640 |
| Reference Allele: TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA | Alternative Allele: TCATGCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA,T,CCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA,ACATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA |
| Primary Allele: TCATGTACCCCGACCTTCAT CAAACATGGATTTTGTGGTT GCTTTGCCTCGTCGGTGCCA | Secondary Allele: TCATGCATGTACCCCGACCT TCATCAAACATGGATTTTGT GGTTGCTTTGCCTCGTCGGT GCCA |
Inferred Ancestral Allele: Not determined.
TGGCTTTGTTTCGCCAAAACCCGGTCACAGTATACTACCATCACGTCGGTGTGCGGAGGGAATTTGGTGAAGGGGTGACCTTTGCCTCGTCGGTGCCCAG[TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA/TCATGCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA,T,CCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA,ACATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA]
AGCAACGGTGTATCCGGTTCCCGTCCATTTTAGACGTGTTAATAATGTAGTGACCTGACCTTGTCGGCACTCAGCCATGGTTTCGTCTAGCCTCATCGGT
ACCGATGAGGCTAGACGAAACCATGGCTGAGTGCCGACAAGGTCAGGTCACTACATTATTAACACGTCTAAAATGGACGGGAACCGGATACACCGTTGCT[TGGCACCGACGAGGCAAAGCAACCACAAAATCCATGTTTGATGAAGGTCGGGGTACATGA/TGGCACCGACGAGGCAAAGCAACCACAAAATCCATGTTTGATGAAGGTCGGGGTACATGCATGA,A,TGGCACCGACGAGGCAAAGCAACCACAAAATCCATGTTTGATGAAGGTCGGGGTACATGG,TGGCACCGACGAGGCAAAGCAACCACAAAATCCATGTTTGATGAAGGTCGGGGTACATGT]
CTGGGCACCGACGAGGCAAAGGTCACCCCTTCACCAAATTCCCTCCGCACACCGACGTGATGGTAGTATACTGTGACCGGGTTTTGGCGAAACAAAGCCA
| Populations | Population Size | Frequency of TCATGTACCCCGACCTTCAT CAAACATGGATTTTGTGGTT GCTTTGCCTCGTCGGTGCCA(primary allele) | Frequency of TCATGCATGTACCCCGACCT TCATCAAACATGGATTTTGT GGTTGCTTTGCCTCGTCGGT GCCA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.90% | 4.90% | 25.88% | 25.45% | T: 1.54%; CCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.28%; ACATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.11% |
| All Indica | 2759 | 10.40% | 7.80% | 39.18% | 40.85% | T: 1.38%; CCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.29%; ACATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.18% |
| All Japonica | 1512 | 92.70% | 0.10% | 3.57% | 1.46% | T: 1.92%; CCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.20% |
| Aus | 269 | 58.00% | 3.30% | 24.54% | 11.52% | T: 1.86%; CCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.74% |
| Indica I | 595 | 10.40% | 4.40% | 42.52% | 39.83% | T: 2.52%; CCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.34% |
| Indica II | 465 | 9.70% | 6.20% | 32.90% | 49.89% | T: 1.29% |
| Indica III | 913 | 7.80% | 11.40% | 40.31% | 39.43% | ACATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.44%; CCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.33%; T: 0.33% |
| Indica Intermediate | 786 | 13.70% | 7.00% | 39.06% | 37.91% | T: 1.78%; CCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.38%; ACATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.13% |
| Temperate Japonica | 767 | 96.70% | 0.10% | 0.91% | 2.09% | T: 0.13% |
| Tropical Japonica | 504 | 85.10% | 0.20% | 7.74% | 0.79% | T: 5.56%; CCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA: 0.60% |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 3.32% | 0.83% | NA |
| VI/Aromatic | 96 | 88.50% | 2.10% | 5.21% | 4.17% | NA |
| Intermediate | 90 | 55.60% | 3.30% | 18.89% | 21.11% | T: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> TCATGCATGTACCCCGACCTTCATCAAACA TGGATTTTGTGGTTGCTTTGCCTCGTCGGT GCCA | LOC_Os06g29700.1 | upstream_gene_variant ; 4525.0bp to feature; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> TCATGCATGTACCCCGACCTTCATCAAACA TGGATTTTGTGGTTGCTTTGCCTCGTCGGT GCCA | LOC_Os06g29690.1 | downstream_gene_variant ; 2730.0bp to feature; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> TCATGCATGTACCCCGACCTTCATCAAACA TGGATTTTGTGGTTGCTTTGCCTCGTCGGT GCCA | LOC_Os06g29690-LOC_Os06g29700 | intergenic_region ; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> ACATGTACCCCGACCTTCATCAAACATGGA TTTTGTGGTTGCTTTGCCTCGTCGGTGCCA | LOC_Os06g29700.1 | upstream_gene_variant ; 4530.0bp to feature; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> ACATGTACCCCGACCTTCATCAAACATGGA TTTTGTGGTTGCTTTGCCTCGTCGGTGCCA | LOC_Os06g29690.1 | downstream_gene_variant ; 2725.0bp to feature; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> ACATGTACCCCGACCTTCATCAAACATGGA TTTTGTGGTTGCTTTGCCTCGTCGGTGCCA | LOC_Os06g29690-LOC_Os06g29700 | intergenic_region ; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> T | LOC_Os06g29700.1 | upstream_gene_variant ; 4529.0bp to feature; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> T | LOC_Os06g29690.1 | downstream_gene_variant ; 2726.0bp to feature; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> T | LOC_Os06g29690-LOC_Os06g29700 | intergenic_region ; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> DEL | N | N | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> CCATGTACCCCGACCTTCATCAAACATGGA TTTTGTGGTTGCTTTGCCTCGTCGGTGCCA | LOC_Os06g29700.1 | upstream_gene_variant ; 4530.0bp to feature; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> CCATGTACCCCGACCTTCATCAAACATGGA TTTTGTGGTTGCTTTGCCTCGTCGGTGCCA | LOC_Os06g29690.1 | downstream_gene_variant ; 2725.0bp to feature; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0617039640 | TCATGTACCCCGACCTTCATCAAACATGGATTTTGTGGTTGCTTTGCCTCGTCGGTGCCA -> CCATGTACCCCGACCTTCATCAAACATGGA TTTTGTGGTTGCTTTGCCTCGTCGGTGCCA | LOC_Os06g29690-LOC_Os06g29700 | intergenic_region ; MODIFIER | silent_mutation | Average:34.134; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0617039640 | 2.38E-06 | NA | mr1229 | 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 |
| vg0617039640 | 6.41E-06 | 1.60E-06 | mr1229 | 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 |
| vg0617039640 | 8.92E-06 | NA | mr1275 | 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 |
| vg0617039640 | NA | 9.60E-06 | mr1992 | 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 |