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Human vs Ferret LastZ alignments

Human (Homo sapiens, GRCh37) and Ferret (Mustela putorius furo, MusPutFur1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 69. Human 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

Human Ferret
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}

Results

Number of alignment blocks: 2,064,918

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 1,583,284,269 out of 3,098,825,702
Covered: 1,515,541,433 out of 3,098,825,702

Uncovered: 1,259,489 out of 35,313,516
Matches: 29,408,059 out of 35,313,516
Mismatches: 4,371,035 out of 35,313,516
Insertions: 274,933 out of 35,313,516

Mustela putorius furo

Uncovered: 975,659,747 out of 2,410,758,013
Covered: 1,435,098,266 out of 2,410,758,013

Uncovered: 1,374,586 out of 31,900,581
Matches: 26,686,564 out of 31,900,581
Mismatches: 3,674,905 out of 31,900,581
Insertions: 164,526 out of 31,900,581