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Human vs Cave fish LastZ alignments

Human (Homo sapiens, GRCh37) and Cave fish (Astyanax mexicanus, AstMex102) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 74. 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)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

Human Cave fish
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}

Results

Number of alignment blocks: 194,397

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

Uncovered: 3,064,756,233 out of 3,098,825,702
Covered: 34,069,469 out of 3,098,825,702

Uncovered: 14,517,780 out of 35,274,750
Matches: 14,288,976 out of 35,274,750
Mismatches: 6,106,123 out of 35,274,750
Insertions: 361,871 out of 35,274,750

Astyanax mexicanus

Uncovered: 1,166,478,691 out of 1,191,242,572
Covered: 24,763,881 out of 1,191,242,572

Uncovered: 19,116,210 out of 36,715,309
Matches: 12,144,418 out of 36,715,309
Mismatches: 5,142,422 out of 36,715,309
Insertions: 312,259 out of 36,715,309