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Human vs Gorilla LastZ alignments

Human (Homo sapiens, GRCh37) and Gorilla (Gorilla gorilla gorilla, gorGor3.1) 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 Gorilla
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: 459,184

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

Uncovered: 507,695,361 out of 3,098,825,702
Covered: 2,591,130,341 out of 3,098,825,702

Uncovered: 1,276,844 out of 35,313,516
Matches: 33,651,273 out of 35,313,516
Mismatches: 353,695 out of 35,313,516
Insertions: 31,704 out of 35,313,516

Gorilla gorilla gorilla

Uncovered: 525,454,843 out of 3,040,677,044
Covered: 2,515,222,201 out of 3,040,677,044

Uncovered: 456,661 out of 32,621,447
Matches: 31,857,567 out of 32,621,447
Mismatches: 285,410 out of 32,621,447
Insertions: 21,809 out of 32,621,447