Lucilia cuprina vs Glossina morsitans LastZ results

Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Glossina morsitans (Glossina morsitans morsitans, GmorY1) 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 morsitans
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 85,544 alignment blocks

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

Uncovered: 399,861,894 out of 434,128,924
Covered: 34,267,030 out of 434,128,924

Uncovered: 4,752,066 out of 22,222,068
Matches: 12,143,741 out of 22,222,068
Mismatches: 4,714,563 out of 22,222,068
Insertions: 611,698 out of 22,222,068
Identity over aligned base-pairs: 69.5%

Glossina morsitans

Uncovered: 330,766,181 out of 366,195,856
Covered: 35,429,675 out of 366,195,856

Uncovered: 2,707,863 out of 20,527,791
Matches: 12,518,261 out of 20,527,791
Mismatches: 4,863,820 out of 20,527,791
Insertions: 437,847 out of 20,527,791
Identity over aligned base-pairs: 70.2%

Block size distribution

Size range All 85,544 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
272
1.6 kb
10 bp - 100 bp
12,850
859.7 kb
5,817
413.2 kb
100 bp - 1 kb
61,097
22.9 Mb
26,761
10.1 Mb
1 kb - 10 kb
11,314
19.8 Mb
9,440
24.1 Mb
10 kb - 100 kb
11
144.4 kb
566
9.0 Mb
100 kb - 1 Mb
1
110.7 kb