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Musca domestica (House fly, aabys) vs Glossina fuscipes (Tsetse fly, IAEA_lab_2018) LastZ results

Musca domestica (House fly, aabys) (Musca domestica, MdomA1) 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. Musca domestica (House fly, aabys) 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

ParameterMusca domestica (House fly, aabys)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 84,649 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Musca domestica (House fly, aabys)

Uncovered: 719,109,475 out of 750,403,944
Covered: 31,294,469 out of 750,403,944

Uncovered: 4,850,916 out of 23,390,585
Matches: 12,648,863 out of 23,390,585
Mismatches: 5,239,346 out of 23,390,585
Insertions: 651,460 out of 23,390,585
Identity over aligned base-pairs: 68.2%

Glossina fuscipes (Tsetse fly, IAEA_lab_2018)

Uncovered: 358,092,649 out of 390,087,113
Covered: 31,994,464 out of 390,087,113

Uncovered: 3,387,834 out of 21,569,001
Matches: 12,599,306 out of 21,569,001
Mismatches: 5,141,775 out of 21,569,001
Insertions: 440,086 out of 21,569,001
Identity over aligned base-pairs: 69.3%

Block size distribution

Size range All 84,649 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
309
1.8 kb
10 bp - 100 bp
10,848
725.0 kb
4,906
350.0 kb
100 bp - 1 kb
63,224
23.7 Mb
29,551
11.2 Mb
1 kb - 10 kb
10,245
17.2 Mb
10,169
24.2 Mb
10 kb - 100 kb
23
365.1 kb
363
6.2 Mb