Variant ID: vg1103982461 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 3982461 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 259. )
ATCTTTATCAAACTTAGCAACCAAACATGTTATCACAGGTGAAACAGGATTTTCAAAATCAGCTTTAAACACTCTTCCATAGCGAGAAATATTCAACATA[G/A]
AATCACCACAAGAATCAAAAACTTTACTTCCAGTTTTCTTAAAGTGAACCTCAAAATTTTCATCAACATTTTGTGAAACTGAAAGCAAATTATACTTTAA
TTAAAGTATAATTTGCTTTCAGTTTCACAAAATGTTGATGAAAATTTTGAGGTTCACTTTAAGAAAACTGGAAGTAAAGTTTTTGATTCTTGTGGTGATT[C/T]
TATGTTGAATATTTCTCGCTATGGAAGAGTGTTTAAAGCTGATTTTGAAAATCCTGTTTCACCTGTGATAACATGTTTGGTTGCTAAGTTTGATAAAGAT
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 91.90% | 7.70% | 0.30% | 0.06% | NA |
All Indica | 2759 | 99.60% | 0.30% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 76.10% | 23.10% | 0.73% | 0.13% | NA |
Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.00% | 0.90% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 91.90% | 7.70% | 0.39% | 0.00% | NA |
Tropical Japonica | 504 | 61.70% | 37.70% | 0.60% | 0.00% | NA |
Japonica Intermediate | 241 | 55.60% | 41.50% | 2.07% | 0.83% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 91.10% | 6.70% | 1.11% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1103982461 | G -> A | LOC_Os11g07800.1 | missense_variant ; p.Ser613Phe; MODERATE | nonsynonymous_codon ; S613F | Average:20.375; most accessible tissue: Minghui63 root, score: 27.443 | benign | 0.282 | DELETERIOUS | 0.05 |
vg1103982461 | G -> DEL | LOC_Os11g07800.1 | N | frameshift_variant | Average:20.375; most accessible tissue: Minghui63 root, score: 27.443 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1103982461 | 1.40E-06 | 1.40E-06 | mr1319 | 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 |
vg1103982461 | NA | 8.10E-06 | mr1579 | Jap_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 |