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To detect nucleosome midpoint positions, sequence data were Gaussian-smoothed as described previously by Shivaswamy et al. (2008) and Kaplan et al. (2009).
The BACs representing the A and C subgenomes were identical in sequence at the site of the assay nucleotide in both cases, but at other positions sequence differences differentiated the subgenomes.
The EnsEMBL gene identities and chromosome positions sequence are listed in the additional data file 3. Sequences were obtained from EnsEMBL v22.1, except for dog sequences (v27.1 – Dec2004) and macaque and cow (v36 – Dec2005).
Assessment of known and putative novel single nucleotide variants (SNVs) was performed on the base of the Roche Reference Mapper software providing high confidence differences (HCDiff) including chromosomal positions, sequence depths, variant's allele frequencies and SNP entry IDs.
Annotations contain various elements such as positions, sequence of the consensus unit, links to related NCBI information, links to graphical circular views of the genome [thanks to CGView, see (Stothard and Wishart, 2005)].
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Finally, because some identifications are based on single nucleotide positions, sequencing errors could cause further false identifications.
Information on physical positions, sequences accession numbers and molecular characteristics were retrieved from corresponding web resources [ 58, 66].
A total of 298 positions sequenced for one individual from each of the 19 Cubitermes colonies, for Apilitermes longiceps and Crenetermes albotarsalis were aligned for ITS2 sequences.
Mean MR was first calculated considering all positions sequenced in this study (853 bp) and then considering all heteroplasmic sites (Table 1).
In these SNP/INDELs position, sequence of KYJ is same to Nipponbare.
According to formula (7), the corresponding saturation position sequence [d 1, d 2, …, d n ] has been calculated.
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