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The resulting map was relatively flat and different in appearance from the breast cancer maps, suggesting no spatial screening bias (map not shown, p-value for global test = 0.18).
The apparent nonrandom distribution of MSVs argues strongly for the development of tools that can be applied for automated scoring (clustering), filtering and mapping of complex SNPs, as discarding such markers will bias map construction and create information gaps in the linkage map.
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To account for the reference bias mapping [ 18], we apply default probabilities p = 0.55 and q = 0.45 (user-specific, see Additional file 1: Figure S1 and Supplementary Methods).
Larson et al. (2012) recommended filtering on the basis of strand bias, mapping quality, proximity to read ends, proximity to indels, nearby homopolymers, nearby SNVs and depth.
VQSR integrates multiple attributes/annotations of the variants, all of which are based on features of sequencing, including the depth of coverage, strand bias, mapping qualities and variant position bias toward the end of the reads.
In addition, sometimes there are problems with the assembly of repetitive elements [ 25], so the lack of ERVs in zebu and yak could be an additive effect of quality of genome sequencing and the usual bias mapping repetitive elements.
In wild-type N2 animals, infection with virus leads to generation of predominantly 23 nt small RNAs with no first nucleotide bias, mapping both sense and antisense to the viral genome in equal proportions.
To avoid model bias, the map was calculated using a simulated annealing omit map at the adduct and its complementary base sites.
Repeatability for the bias of MAP (1.96 × SD of the difference between repeated measurements) was 6.9 mmHg.
This person was blinded to the identity of the electrode being mapped, and the electrodes were always mapped in random order to prevent bias when mapping receptive fields.
Figure 4 shows some results for an unbiased, a feature biased and a feature and location biased saliency map.
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