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Human vs Bushbaby LastZ alignments

Human (Homo sapiens, GRCh37) and Bushbaby (Otolemur garnettii, OtoGar3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 65. 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)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)50
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 Bushbaby
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: 2,087,975

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

Uncovered: 1,534,705,086 out of 3,098,825,702
Covered: 1,564,120,616 out of 3,098,825,702

Uncovered: 950,705 out of 35,313,516
Matches: 30,227,943 out of 35,313,516
Mismatches: 3,876,162 out of 35,313,516
Insertions: 258,706 out of 35,313,516

Otolemur garnettii

Uncovered: 1,057,693,960 out of 2,519,404,493
Covered: 1,461,710,533 out of 2,519,404,493

Uncovered: 1,624,068 out of 31,659,618
Matches: 26,836,196 out of 31,659,618
Mismatches: 3,101,707 out of 31,659,618
Insertions: 97,647 out of 31,659,618