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Human vs Squirrel LastZ alignments

Human (Homo sapiens, GRCh37) and Squirrel (Ictidomys tridecemlineatus, spetri2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 67. 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 Squirrel
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: 1,977,251

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

Uncovered: 1,619,166,522 out of 3,098,825,702
Covered: 1,479,659,180 out of 3,098,825,702

Uncovered: 1,379,288 out of 35,313,516
Matches: 29,421,182 out of 35,313,516
Mismatches: 4,215,620 out of 35,313,516
Insertions: 297,426 out of 35,313,516

Ictidomys tridecemlineatus

Uncovered: 1,099,113,939 out of 2,478,393,770
Covered: 1,379,279,831 out of 2,478,393,770

Uncovered: 1,453,006 out of 28,885,868
Matches: 24,190,525 out of 28,885,868
Mismatches: 3,142,045 out of 28,885,868
Insertions: 100,292 out of 28,885,868