Deletions

5kb deletion (hetero) in Chromosome 3

17kb deletion (hetero) in Chromosome 8

Transgene related

Acrosin

Large coverage in upstream and a part of its coding region indicates that this region is used as a transgene and multiple copies are inserted in the genome.

Mean coverage in this 2.4-kb region was 108.4.

$ samtools mpileup -f ../../genome/Mus_musculus.GRCm38.74.dna.toplevel.fa.gz DRR028646.bam -r15:89566016-89568433 \
$ 	awk '{sum=+$4} END {print sum/NR}'

Mean coverages of the flanking 2.4-kb regions of Acrsin promoter region was 11.4 and 11.1. Genome has 2 copies of acrosin promoter region and thus exptected coverage of the 2.4-kb region relative to its surrounding region is (n + 2)/2, where n is the copy number of acrosin promoters in the inserted transgenes. From this model, I can estimate n = 17.

Oct4

There's no indication of the use of Oct4 promoter as a transgene in thie genome.