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To ensure maximum genome coverage, 164 markers were selected for population mapping using published consensus maps [[ 21]] aiming for a marker density every 20 cM where possible.
The maximum genome coverage of the markers described in this study was estimated to be 1187 cM (887 + 200 + 100 cM) (see[ 56, 57]), covering about a third of the Siberian jay genome of ~3800 cM, if estimated by assuming a similar genome size as in chicken [ 54].
That DRIMM scores poorly under both schemes, however, is due to a different set of goals: as stated by the authors, DRIMM aims at maximum genome coverage and simply ignores discordant homologies and other conditions that would cause Cyntenator or i-ADHoRe to break a block.
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Two recent studies, investigated the cost, genome coverage, maximum resolution, and quality measures for a variety of NGS approaches as applied to DNA methylation.
The threshold to declare a ROH was set to a SNP count maximum of 0.25x the genome coverage following Bosse et al. [ 15].
The numbers of mapped reads, genome coverage, depth, and maximum contig length are reported.
Figure 5 shows how the N50 value and the genome coverage evolve when the maximum size of the biconnected component is varied.
There was a large variation in the lengths of individual linkage groups that varied from a maximum of 205.4 cM to a minimum of 29.8 cM and genome coverage varying from 96.0% (LG6) to 33.0% (LG3).
To reduce the bias of collapsed regions, the maximum number of reads mapped in a SNP position was set to double the genome coverage of the corresponding genome.
There are two possible strategies to overcome uneven genome coverage.
The genome coverage was 88.5% and included 37,758 genes.
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