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Glossina morsitans morsitans (Tsetse fly, Yale) vs Stomoxys calcitrans (Stable fly, USDA) LastZ results

Glossina morsitans morsitans (Tsetse fly, Yale) (Glossina morsitans morsitans, GmorY1) and Stomoxys calcitrans (Stable fly, USDA) (Stomoxys calcitrans, ScalU1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 99. Glossina morsitans morsitans (Tsetse fly, Yale) 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

ParameterGlossina morsitans morsitans (Tsetse fly, Yale)Stomoxys calcitrans (Stable fly, USDA)
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 76,121 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Glossina morsitans morsitans (Tsetse fly, Yale)

Uncovered: 337,997,790 out of 366,195,856
Covered: 28,198,066 out of 366,195,856

Uncovered: 3,517,690 out of 20,527,791
Matches: 11,778,528 out of 20,527,791
Mismatches: 4,829,114 out of 20,527,791
Insertions: 402,459 out of 20,527,791
Identity over aligned base-pairs: 69.2%

Stomoxys calcitrans (Stable fly, USDA)

Uncovered: 943,392,251 out of 971,188,624
Covered: 27,796,373 out of 971,188,624

Uncovered: 5,135,602 out of 23,712,588
Matches: 12,681,443 out of 23,712,588
Mismatches: 5,270,912 out of 23,712,588
Insertions: 624,631 out of 23,712,588
Identity over aligned base-pairs: 68.3%

Block size distribution

Size range All 76,121 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
196
1.2 kb
10 bp - 100 bp
12,024
795.5 kb
5,881
406.7 kb
100 bp - 1 kb
55,758
20.2 Mb
27,439
10.1 Mb
1 kb - 10 kb
8,139
13.4 Mb
8,361
20.0 Mb
10 kb - 100 kb
4
53.6 kb
257
4.0 Mb