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Mouse vs Platypus LastZ alignments

Mouse (Mus musculus, GRCm38) and Platypus (Ornithorhynchus anatinus, OANA5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 68. Mouse was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

Mouse Platypus
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}

Results

Number of alignment blocks: 322,976

Genome coverage (bp) Coding exon coverage (bp)
Mus musculus

Uncovered: 2,639,818,068 out of 2,730,871,774
Covered: 91,053,706 out of 2,730,871,774

Uncovered: 8,716,655 out of 35,991,038
Matches: 20,085,749 out of 35,991,038
Mismatches: 6,890,021 out of 35,991,038
Insertions: 298,613 out of 35,991,038

Ornithorhynchus anatinus

Uncovered: 1,995,931,113 out of 2,073,148,626
Covered: 77,217,513 out of 2,073,148,626

Uncovered: 5,525,803 out of 24,997,756
Matches: 14,564,827 out of 24,997,756
Mismatches: 4,676,489 out of 24,997,756
Insertions: 230,637 out of 24,997,756