Lucilia cuprina vs Glossina palpalis LastZ results

Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Glossina palpalis (Glossina palpalis gambiensis, GpapI1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 99. Lucilia cuprina was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
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

ParameterLucilia cuprinaGlossina palpalis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 87,438 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Lucilia cuprina

Uncovered: 398,160,433 out of 434,128,924
Covered: 35,968,491 out of 434,128,924

Uncovered: 4,804,220 out of 22,222,068
Matches: 11,981,902 out of 22,222,068
Mismatches: 4,829,422 out of 22,222,068
Insertions: 606,524 out of 22,222,068
Identity over aligned base-pairs: 68.8%

Glossina palpalis

Uncovered: 342,167,311 out of 380,104,241
Covered: 37,936,930 out of 380,104,241

Uncovered: 4,989,704 out of 24,086,735
Matches: 13,352,378 out of 24,086,735
Mismatches: 5,265,636 out of 24,086,735
Insertions: 479,017 out of 24,086,735
Identity over aligned base-pairs: 69.9%

Block size distribution

Size range All 87,438 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
282
1.6 kb
10 bp - 100 bp
12,834
854.0 kb
5,936
419.0 kb
100 bp - 1 kb
61,738
23.1 Mb
27,210
10.0 Mb
1 kb - 10 kb
12,569
23.3 Mb
9,953
25.9 Mb
10 kb - 100 kb
15
183.6 kb
638
11.1 Mb