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Mouse vs Chicken LastZ alignments

Mouse (Mus musculus, GRCm38) and Chicken (Gallus gallus, Galgal4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 71. 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)3000
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 Chicken
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: 277,540

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

Uncovered: 2,662,166,664 out of 2,730,871,774
Covered: 68,705,110 out of 2,730,871,774

Uncovered: 9,706,852 out of 35,991,038
Matches: 19,006,763 out of 35,991,038
Mismatches: 6,921,261 out of 35,991,038
Insertions: 356,162 out of 35,991,038

Gallus gallus

Uncovered: 991,521,861 out of 1,046,932,099
Covered: 55,410,238 out of 1,046,932,099

Uncovered: 4,611,115 out of 25,934,237
Matches: 15,695,237 out of 25,934,237
Mismatches: 5,381,883 out of 25,934,237
Insertions: 246,002 out of 25,934,237