Maximum, average, and median gaps were calculated for each analysis based on genomic position of SNP on the bovine UMD3.1 genome assembly.
For details on the resulting 244 CNVRs based on 8051 CNV markers with genomic positions based on genome build hg 18 (March 2006), see Table 1 and Figure 2.
We retrieved alignments of all protein sequences from C. elegans, C. briggsae, C. remanei, C. brenneri, and C. japonica and re-inserted intron positions based on genome annotations.
As the reference SNP (refSNP) position information of O. sativa provided on dbSNP is based on genome build 3. We redefined the SNP position information based on build 5. To update the refSNP to genome build 5, we reconstructed the refSNP position information based on 4,521,605 refSNPs reported in dbSNP (Table 5).
At position 11, the motif varies based on genome size.
Candidate genes were identified by position based on the Wellcome Trust Sanger mouse genomes database, www.sanger.ac.uk, release 1303, based on genome assembly GRCm38 (Yalcin et al. 2011).
In order to assess the extent of variability that the KWP1 genome exhibits, we performed inter-genome comparisons with 10 representative genomes from four continents and derived nearest-neighbor tree based on genome-wide variant positions shared among genomes.
Seven previously unnanotated ORFs could in fact be some remnants of ribosomal protein genes, based on its genome position and considering some degree of synteny with other completely sequenced γ-proteobacteria, but only three of them (rplQ, rpsE, and rpsO) retain enough homology to be annotated as such.
To compare nickel-treated versus control H3K4me3 ChIP data sets, the two lists of peaks were matched based on overlapped genome positions.
The approximate coordinates were found based on the genome positions of BAC and cDNA clones, which were physically mapped to chromosomes near heterochromatin-euchromatin boundaries [ 44, 55].
