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Glossina morsitans morsitans (Tsetse fly, Yale) vs Glossina fuscipes (Tsetse fly, IAEA_lab_2018) LastZ results

Glossina morsitans morsitans (Tsetse fly, Yale) (Glossina morsitans morsitans, GmorY1) 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. 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)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 459,567 alignment blocks

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

Uncovered: 54,400,797 out of 366,195,856
Covered: 311,795,059 out of 366,195,856

Uncovered: 312,923 out of 20,559,057
Matches: 18,703,443 out of 20,559,057
Mismatches: 1,452,685 out of 20,559,057
Insertions: 90,006 out of 20,559,057
Identity over aligned base-pairs: 92.4%

Glossina fuscipes (Tsetse fly, IAEA_lab_2018)

Uncovered: 62,663,130 out of 390,087,113
Covered: 327,423,983 out of 390,087,113

Uncovered: 163,083 out of 21,569,001
Matches: 20,133,273 out of 21,569,001
Mismatches: 1,202,322 out of 21,569,001
Insertions: 70,323 out of 21,569,001
Identity over aligned base-pairs: 94.1%

Block size distribution

Size range All 459,567 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7,612
46.5 kb
10 bp - 100 bp
77,653
4.7 Mb
26,336
1.8 Mb
100 bp - 1 kb
262,685
100.3 Mb
90,513
32.5 Mb
1 kb - 10 kb
110,846
265.0 Mb
26,133
57.6 Mb
10 kb - 100 kb
771
10.3 Mb
4,012
140.9 Mb
100 kb - 1 Mb
610
118.5 Mb
1 Mb - 10 Mb
19
28.9 Mb