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Human vs Cat LastZ alignments

Human (Homo sapiens, GRCh37) and Cat (Felis catus, Felis_catus_6.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 70. 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 Cat
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: 2,189,498

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

Uncovered: 1,547,591,241 out of 3,098,825,702
Covered: 1,551,234,461 out of 3,098,825,702

Uncovered: 1,520,158 out of 35,313,516
Matches: 29,344,279 out of 35,313,516
Mismatches: 4,163,997 out of 35,313,516
Insertions: 285,082 out of 35,313,516

Felis catus

Uncovered: 986,475,634 out of 2,455,541,136
Covered: 1,469,065,502 out of 2,455,541,136

Uncovered: 1,155,158 out of 30,851,959
Matches: 26,237,896 out of 30,851,959
Mismatches: 3,330,081 out of 30,851,959
Insertions: 128,824 out of 30,851,959