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Human vs Gibbon LastZ alignments

Human (Homo sapiens, GRCh37) and Gibbon (Nomascus leucogenys, Nleu1.0) 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 Gibbon
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: 544,826

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

Uncovered: 544,022,468 out of 3,098,825,702
Covered: 2,554,803,234 out of 3,098,825,702

Uncovered: 1,470,166 out of 35,313,516
Matches: 33,042,773 out of 35,313,516
Mismatches: 733,997 out of 35,313,516
Insertions: 66,580 out of 35,313,516

Nomascus leucogenys

Uncovered: 472,999,579 out of 2,936,035,333
Covered: 2,463,035,754 out of 2,936,035,333

Uncovered: 411,014 out of 30,035,029
Matches: 29,046,838 out of 30,035,029
Mismatches: 549,786 out of 30,035,029
Insertions: 27,391 out of 30,035,029