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Human vs Marmoset LastZ alignments

Human (Homo sapiens, GRCh37) and Marmoset (Callithrix jacchus, C_jacchus3.2.1) 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 Marmoset
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: 1,419,752

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

Uncovered: 959,732,396 out of 3,098,825,702
Covered: 2,139,093,306 out of 3,098,825,702

Uncovered: 1,320,970 out of 35,313,516
Matches: 32,047,157 out of 35,313,516
Mismatches: 1,749,448 out of 35,313,516
Insertions: 195,941 out of 35,313,516

Callithrix jacchus

Uncovered: 870,174,352 out of 2,914,958,544
Covered: 2,044,784,192 out of 2,914,958,544

Uncovered: 2,017,153 out of 33,607,040
Matches: 29,902,114 out of 33,607,040
Mismatches: 1,572,848 out of 33,607,040
Insertions: 114,925 out of 33,607,040