Lucilia cuprina vs Glossina pallidipes LastZ results

Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Glossina pallidipes (Glossina pallidipes, GpalI1) 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 pallidipes
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 89,399 alignment blocks

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

Uncovered: 398,060,105 out of 434,128,924
Covered: 36,068,819 out of 434,128,924

Uncovered: 4,703,821 out of 22,222,068
Matches: 12,157,023 out of 22,222,068
Mismatches: 4,748,247 out of 22,222,068
Insertions: 612,977 out of 22,222,068
Identity over aligned base-pairs: 69.4%

Glossina pallidipes

Uncovered: 320,476,217 out of 357,332,231
Covered: 36,856,014 out of 357,332,231

Uncovered: 5,075,820 out of 22,910,370
Matches: 12,466,032 out of 22,910,370
Mismatches: 4,921,920 out of 22,910,370
Insertions: 446,598 out of 22,910,370
Identity over aligned base-pairs: 69.9%

Block size distribution

Size range All 89,399 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
289
1.7 kb
10 bp - 100 bp
13,199
869.1 kb
5,806
400.7 kb
100 bp - 1 kb
63,760
23.9 Mb
27,166
10.2 Mb
1 kb - 10 kb
12,136
21.7 Mb
9,634
24.2 Mb
10 kb - 100 kb
15
193.0 kb
639
11.7 Mb
100 kb - 1 Mb
1
116.5 kb