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Medaka vs Cave fish LastZ alignments

Medaka (Oryzias latipes, MEDAKA1) and Cave fish (Astyanax mexicanus, AstMex102) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 74. Medaka 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

Medaka 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: 311,425

Genome coverage (bp) Coding exon coverage (bp)
Oryzias latipes

Uncovered: 800,163,141 out of 869,000,216
Covered: 68,837,075 out of 869,000,216

Uncovered: 5,068,799 out of 30,205,021
Matches: 18,157,253 out of 30,205,021
Mismatches: 6,591,598 out of 30,205,021
Insertions: 387,371 out of 30,205,021

Astyanax mexicanus

Uncovered: 1,144,629,733 out of 1,191,242,572
Covered: 46,612,839 out of 1,191,242,572

Uncovered: 11,911,882 out of 36,715,309
Matches: 17,783,003 out of 36,715,309
Mismatches: 6,572,160 out of 36,715,309
Insertions: 448,264 out of 36,715,309