Lucilia cuprina vs Glossina austeni LastZ results

Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Glossina austeni (Glossina austeni, GausT1) 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 austeni
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 88,816 alignment blocks

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

Uncovered: 397,882,988 out of 434,128,924
Covered: 36,245,936 out of 434,128,924

Uncovered: 4,763,849 out of 22,222,068
Matches: 12,098,365 out of 22,222,068
Mismatches: 4,751,912 out of 22,222,068
Insertions: 607,942 out of 22,222,068
Identity over aligned base-pairs: 69.3%

Glossina austeni

Uncovered: 333,334,520 out of 370,264,922
Covered: 36,930,402 out of 370,264,922

Uncovered: 5,507,030 out of 23,999,935
Matches: 12,900,348 out of 23,999,935
Mismatches: 5,121,307 out of 23,999,935
Insertions: 471,250 out of 23,999,935
Identity over aligned base-pairs: 69.8%

Block size distribution

Size range All 88,816 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
325
1.9 kb
10 bp - 100 bp
13,293
886.7 kb
6,160
435.9 kb
100 bp - 1 kb
62,941
23.7 Mb
26,759
10.1 Mb
1 kb - 10 kb
12,243
22.1 Mb
9,917
24.9 Mb
10 kb - 100 kb
14
190.2 kb
637
11.5 Mb