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Glossina morsitans morsitans (Tsetse fly, Yale) vs Musca domestica (House fly, aabys) LastZ results

Glossina morsitans morsitans (Tsetse fly, Yale) (Glossina morsitans morsitans, GmorY1) and Musca domestica (House fly, aabys) (Musca domestica, MdomA1) 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)Musca domestica (House fly, aabys)
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 74,842 alignment blocks

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

Uncovered: 338,182,116 out of 366,195,856
Covered: 28,013,740 out of 366,195,856

Uncovered: 3,578,820 out of 20,527,791
Matches: 11,744,408 out of 20,527,791
Mismatches: 4,806,400 out of 20,527,791
Insertions: 398,163 out of 20,527,791
Identity over aligned base-pairs: 69.3%

Musca domestica (House fly, aabys)

Uncovered: 721,014,237 out of 750,403,944
Covered: 29,389,707 out of 750,403,944

Uncovered: 4,887,413 out of 23,391,356
Matches: 12,660,993 out of 23,391,356
Mismatches: 5,193,755 out of 23,391,356
Insertions: 649,195 out of 23,391,356
Identity over aligned base-pairs: 68.4%

Block size distribution

Size range All 74,842 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
268
1.6 kb
10 bp - 100 bp
10,166
676.6 kb
4,661
328.3 kb
100 bp - 1 kb
55,509
20.7 Mb
25,163
9.5 Mb
1 kb - 10 kb
8,894
14.8 Mb
8,880
21.7 Mb
10 kb - 100 kb
5
64.9 kb
306
4.7 Mb