Variant ID: vg1004685372 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 4685372 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TACTTGAGAAGTGCTCATCTCTCCCGGTTCGCAACCCCCTTTACTCCCGGGTAGCGAATCGGGAGGGAGAATCCGGGACTAAAGATGACGGTCTTTAGTC[C/T]
CGGTTCAAATACCCAGGAGTAAATCTCCATCTTTAGTCCCGGTTGGTGACACCAACCGGGACTAAAGATGGCTGAGCCACGTGACCGGCAAAGCCATAAC
GTTATGGCTTTGCCGGTCACGTGGCTCAGCCATCTTTAGTCCCGGTTGGTGTCACCAACCGGGACTAAAGATGGAGATTTACTCCTGGGTATTTGAACCG[G/A]
GACTAAAGACCGTCATCTTTAGTCCCGGATTCTCCCTCCCGATTCGCTACCCGGGAGTAAAGGGGGTTGCGAACCGGGAGAGATGAGCACTTCTCAAGTA
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 | 94.30% | 3.10% | 0.02% | 2.60% | NA |
All Indica | 2759 | 96.40% | 0.00% | 0.00% | 3.55% | NA |
All Japonica | 1512 | 90.30% | 9.50% | 0.00% | 0.20% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.10% | 0.00% | 0.00% | 0.86% | NA |
Indica III | 913 | 91.80% | 0.00% | 0.00% | 8.21% | NA |
Indica Intermediate | 786 | 97.50% | 0.10% | 0.00% | 2.42% | NA |
Temperate Japonica | 767 | 89.70% | 10.30% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 76.30% | 22.40% | 0.00% | 1.24% | NA |
VI/Aromatic | 96 | 78.10% | 1.00% | 0.00% | 20.83% | NA |
Intermediate | 90 | 94.40% | 2.20% | 1.11% | 2.22% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1004685372 | C -> T | LOC_Os10g08630.1 | upstream_gene_variant ; 83.0bp to feature; MODIFIER | silent_mutation | Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 | N | N | N | N |
vg1004685372 | C -> T | LOC_Os10g08640.1 | upstream_gene_variant ; 288.0bp to feature; MODIFIER | silent_mutation | Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 | N | N | N | N |
vg1004685372 | C -> T | LOC_Os10g08620.1 | downstream_gene_variant ; 2478.0bp to feature; MODIFIER | silent_mutation | Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 | N | N | N | N |
vg1004685372 | C -> T | LOC_Os10g08650.1 | downstream_gene_variant ; 2598.0bp to feature; MODIFIER | silent_mutation | Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 | N | N | N | N |
vg1004685372 | C -> T | LOC_Os10g08630-LOC_Os10g08640 | intergenic_region ; MODIFIER | silent_mutation | Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 | N | N | N | N |
vg1004685372 | C -> DEL | N | N | silent_mutation | Average:67.549; most accessible tissue: Minghui63 panicle, score: 91.41 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1004685372 | 3.32E-06 | 3.32E-06 | mr1647_2 | Jap_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 |