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Human vs Orangutan LastZ alignments

Human (Homo sapiens, GRCh37) and Orangutan (Pongo abelii, PPYG2) 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 Orangutan
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: 548,320

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

Uncovered: 450,020,728 out of 3,098,825,702
Covered: 2,648,804,974 out of 3,098,825,702

Uncovered: 940,768 out of 35,313,516
Matches: 33,693,016 out of 35,313,516
Mismatches: 623,154 out of 35,313,516
Insertions: 56,578 out of 35,313,516

Pongo abelii

Uncovered: 878,382,013 out of 3,446,771,396
Covered: 2,568,389,383 out of 3,446,771,396

Uncovered: 563,797 out of 30,528,077
Matches: 29,449,762 out of 30,528,077
Mismatches: 488,131 out of 30,528,077
Insertions: 26,387 out of 30,528,077