The position of each centromere was taken as: 15,088,987 bp on chromosome 1; 3,608,427 bp on chromosome 2; 13,599,567 bp on chromosome 3; 3,456,519 bp on chromosome 4 and 11,742,755 bp on chromosome 5. Affymetrix gene expression data was analysed as described above, although only 1,913 of the genes lacking an insertion were present on the array.
Mammalian sequences for INSL4 were not included in the analysis because the gene contains a large insertion, is present only in mammals, and was the subject of a previous bioinformatic analysis [ 9].
Given that a TE insertion is present in some of the North American strain pools and absent from others (i.e. given its pool frequency), we wished to calculate the likeliest frequency of this insertion in the entire North American population, as well as suitable confidence bounds around such a frequency estimate.
The OH1987 virus differs from HKU15-155 in the spike gene at nt 19469 and in the noncoding region at nt 25044; a 3-nt insertion is present at each location, making the whole-genome sequence of the OH1987 virus 6 nt longer than that of HKU15-155.
An information scar of a single nucleotide "T" insertion is present at the junction.
Thus, when a sequence matched a specific proviral sequence we are not stating that the exact proviral insertion is present in a given mouse, but that the viral lineage that gave rise to that provirus is present.
Interestingly, in the Nichols genome, this insertion is present only in a smaller part of treponemal population [22], suggesting that this region could be deleted without markedly decreasing fitness.
Non-mammalian inhibin α-subunits (i.e., those from fish, amphibians, reptiles, and birds) lack the wrist region insertion but some type of wrist region insertion is present in all known mammalian inhibin α-subunits (Figs. 2A, 2C and S2D).
If the insertion is present in Pantherinae, then the insertion must have occurred in the ancestor of all Felidae.
This apparently derived insertion is present in all the Chloroflexi, which is not discussed by the authors.
