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Human vs Chimpanzee LastZ alignments

Human (Homo sapiens, GRCh37) and Chimpanzee (Pan troglodytes, CHIMP2.1.4) 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

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 Chimpanzee
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}


Number of alignment blocks: 286,994

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

Uncovered: 354,426,780 out of 3,098,825,702
Covered: 2,744,398,922 out of 3,098,825,702

Uncovered: 889,707 out of 35,313,516
Matches: 34,129,430 out of 35,313,516
Mismatches: 261,781 out of 35,313,516
Insertions: 32,598 out of 35,313,516

Pan troglodytes

Uncovered: 622,446,783 out of 3,309,561,368
Covered: 2,687,114,585 out of 3,309,561,368

Uncovered: 273,368 out of 30,309,842
Matches: 29,832,061 out of 30,309,842
Mismatches: 194,290 out of 30,309,842
Insertions: 10,123 out of 30,309,842