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Human vs Macaque LastZ alignments

Human (Homo sapiens, GRCh37) and Macaque (Macaca mulatta, MMUL_1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 66. 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
Seed and Transition value (T)1
Scoring matrix (Q)$ENSEMBL_CVS_ROOT_DIR/ensembl-compara/scripts/pipeline/primate.matrix

Chunking parameters

Human Macaque
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: 827,617

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

Uncovered: 613,486,335 out of 3,098,825,702
Covered: 2,485,339,367 out of 3,098,825,702

Uncovered: 867,403 out of 35,313,516
Matches: 33,299,264 out of 35,313,516
Mismatches: 1,069,593 out of 35,313,516
Insertions: 77,256 out of 35,313,516

Macaca mulatta

Uncovered: 700,290,685 out of 3,097,179,960
Covered: 2,396,889,275 out of 3,097,179,960

Uncovered: 995,354 out of 32,460,852
Matches: 30,476,252 out of 32,460,852
Mismatches: 935,757 out of 32,460,852
Insertions: 53,489 out of 32,460,852