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In this case, the re-aligned soft clips will be placed on locus A and C omitting B as soft clips of the re-aligned locus.
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There are 7 loci placed on our RH map (3 of them are framework loci), which are currently assigned to other than BTA6 specific sequence contigs.
Among the 8681 loci placed on the integrated haploid/diploid female map, diploid family 1, 2, and 3 had 846, 814, and 879 polymorphic loci in common for each male parent.
Of the 10 944 filtered loci, 1156 were successfully placed on the linkage map (33% of loci on the map successfully aligned to one of the 10 944 loci discovered in populations from western Alaska, see Table S1 for map location of successful alignments).
The total map length was 1335.7 cM, based on 276 markers across the genome (179 ddRADs, 13 microsatellites, 84 highly differentiated RNAseq loci); an additional 51 loci were placed on the X chromosome but not ordered on the map.
The largest number of new marker loci (19) was placed on linkage group B01 but an average of 11 new loci were placed on each linkage group.
However, these marker loci are placed on chromosome 5 in the Btau_2.0 sequence assembly.
Linkage group lengths ranged from 171.8 cM (b09k) to 80.8 cM (b07a) and a greater number of BMb loci were placed on b08f (14), and b02d (12) and a lower number on b06g (5) compared to other linkage groups.
We detected nine pairs of duplicated loci where only one of the two loci was polymorphic and placed on the map.
The sex-determining locus has been placed on Chromosome 1 (see Table S3) (Ellis and Janick 1960).
The resulting loci were randomly placed on the mouse genome with mapped CIS inserts or inserts outside of CISs and any cases of overlap were counted.
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