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Zebrafish vs Cave fish LastZ alignments

Zebrafish (Danio rerio, Zv9) and Cave fish (Astyanax mexicanus, AstMex102) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 74. Zebrafish 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

Zebrafish 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} {default_soft_masking => 1}

Results

Number of alignment blocks: 414,859

Genome coverage (bp) Coding exon coverage (bp)
Danio rerio

Uncovered: 1,299,330,211 out of 1,412,464,843
Covered: 113,134,632 out of 1,412,464,843

Uncovered: 5,615,848 out of 42,682,327
Matches: 27,589,616 out of 42,682,327
Mismatches: 9,058,351 out of 42,682,327
Insertions: 418,512 out of 42,682,327

Astyanax mexicanus

Uncovered: 1,098,490,902 out of 1,191,242,572
Covered: 92,751,670 out of 1,191,242,572

Uncovered: 7,104,967 out of 36,715,309
Matches: 22,202,712 out of 36,715,309
Mismatches: 6,907,012 out of 36,715,309
Insertions: 500,618 out of 36,715,309