Lucilia cuprina vs Glossina fuscipes fuscipes LastZ results

Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Glossina fuscipes fuscipes (Glossina fuscipes fuscipes, GfusI1) 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 fuscipes fuscipes
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 88,549 alignment blocks

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

Uncovered: 398,707,480 out of 434,128,924
Covered: 35,421,444 out of 434,128,924

Uncovered: 4,704,493 out of 22,222,068
Matches: 12,129,470 out of 22,222,068
Mismatches: 4,776,351 out of 22,222,068
Insertions: 611,754 out of 22,222,068
Identity over aligned base-pairs: 69.2%

Glossina fuscipes fuscipes

Uncovered: 337,273,557 out of 374,774,708
Covered: 37,501,151 out of 374,774,708

Uncovered: 5,317,030 out of 23,696,776
Matches: 12,838,038 out of 23,696,776
Mismatches: 5,082,811 out of 23,696,776
Insertions: 458,897 out of 23,696,776
Identity over aligned base-pairs: 69.8%

Block size distribution

Size range All 88,549 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
285
1.7 kb
10 bp - 100 bp
12,773
843.1 kb
5,557
388.1 kb
100 bp - 1 kb
63,497
23.9 Mb
27,304
10.3 Mb
1 kb - 10 kb
11,982
21.6 Mb
9,577
24.3 Mb
10 kb - 100 kb
12
147.6 kb
636
11.4 Mb
100 kb - 1 Mb
1
147.1 kb