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Stomoxys calcitrans (Stable fly, USDA) vs Glossina fuscipes (Tsetse fly, IAEA_lab_2018) LastZ results

Stomoxys calcitrans (Stable fly, USDA) (Stomoxys calcitrans, ScalU1) and Glossina fuscipes (Tsetse fly, IAEA_lab_2018) (Glossina fuscipes, Yale_Gfus_2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 106. Stomoxys calcitrans (Stable fly, USDA) 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

ParameterStomoxys calcitrans (Stable fly, USDA)Glossina fuscipes (Tsetse fly, IAEA_lab_2018)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 87,588 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Stomoxys calcitrans (Stable fly, USDA)

Uncovered: 942,581,683 out of 971,188,624
Covered: 28,606,941 out of 971,188,624

Uncovered: 5,152,190 out of 23,734,772
Matches: 12,656,418 out of 23,734,772
Mismatches: 5,306,926 out of 23,734,772
Insertions: 619,238 out of 23,734,772
Identity over aligned base-pairs: 68.1%

Glossina fuscipes (Tsetse fly, IAEA_lab_2018)

Uncovered: 356,286,903 out of 390,087,113
Covered: 33,800,210 out of 390,087,113

Uncovered: 3,325,560 out of 21,569,001
Matches: 12,629,126 out of 21,569,001
Mismatches: 5,175,197 out of 21,569,001
Insertions: 439,118 out of 21,569,001
Identity over aligned base-pairs: 69.2%

Block size distribution

Size range All 87,588 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
214
1.2 kb
10 bp - 100 bp
13,201
882.5 kb
6,589
462.4 kb
100 bp - 1 kb
64,568
23.2 Mb
32,696
11.9 Mb
1 kb - 10 kb
9,566
16.0 Mb
9,655
22.8 Mb
10 kb - 100 kb
39
639.9 kb
323
5.5 Mb