Variant ID: vg0601102379 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 1102379 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 126. )
GTCCTCTTAACTGATGTGCGGCGTAAAGGGTTTTCTCTTGCGGAGTACACTGTACCAGATTTAATTTCCTTTCCATATCTTTAATCCAATCATCAGCTTC[A/G]
ATAGGCTCATTTGTTTGGGAGAACTCCGGTGGACGAGATCCCAAGAAATCATTCAGTTTCGATTGGCCATCATCTTGAACCATATGGGGTTGACGCTCTT
AAGAGCGTCAACCCCATATGGTTCAAGATGATGGCCAATCGAAACTGAATGATTTCTTGGGATCTCGTCCACCGGAGTTCTCCCAAACAAATGAGCCTAT[T/C]
GAAGCTGATGATTGGATTAAAGATATGGAAAGGAAATTAAATCTGGTACAGTGTACTCCGCAAGAGAAAACCCTTTACGCCGCACATCAGTTAAGAGGAC
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 88.90% | 2.00% | 0.97% | 8.13% | NA |
All Indica | 2759 | 88.10% | 3.30% | 1.52% | 7.03% | NA |
All Japonica | 1512 | 98.70% | 0.00% | 0.07% | 1.19% | NA |
Aus | 269 | 38.30% | 0.00% | 1.12% | 60.59% | NA |
Indica I | 595 | 92.40% | 0.30% | 0.00% | 7.23% | NA |
Indica II | 465 | 91.60% | 7.30% | 0.22% | 0.86% | NA |
Indica III | 913 | 83.10% | 1.90% | 3.72% | 11.28% | NA |
Indica Intermediate | 786 | 88.70% | 4.80% | 0.89% | 5.60% | NA |
Temperate Japonica | 767 | 99.20% | 0.00% | 0.13% | 0.65% | NA |
Tropical Japonica | 504 | 97.60% | 0.00% | 0.00% | 2.38% | NA |
Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
VI/Aromatic | 96 | 93.80% | 0.00% | 0.00% | 6.25% | NA |
Intermediate | 90 | 94.40% | 2.20% | 0.00% | 3.33% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0601102379 | A -> G | LOC_Os06g03000.1 | synonymous_variant ; p.Ile124Ile; LOW | synonymous_codon | Average:28.322; most accessible tissue: Zhenshan97 root, score: 47.644 | N | N | N | N |
vg0601102379 | A -> DEL | LOC_Os06g03000.1 | N | frameshift_variant | Average:28.322; most accessible tissue: Zhenshan97 root, score: 47.644 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0601102379 | NA | 6.60E-08 | mr1310 | 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 |
vg0601102379 | 1.71E-06 | 1.71E-06 | mr1926 | 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 |
vg0601102379 | NA | 4.20E-06 | mr1449_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 |
vg0601102379 | NA | 6.18E-08 | mr1712_2 | 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 |
vg0601102379 | 5.64E-06 | 1.88E-07 | mr1717_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 |
vg0601102379 | NA | 2.26E-06 | mr1733_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 |