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Musca domestica (House fly, aabys) vs Stomoxys calcitrans (Stable fly, USDA) LastZ results

Musca domestica (House fly, aabys) (Musca domestica, MdomA1) and Stomoxys calcitrans (Stable fly, USDA) (Stomoxys calcitrans, ScalU1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 99. 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)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 222,380 alignment blocks

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

Uncovered: 658,818,626 out of 750,403,944
Covered: 91,585,318 out of 750,403,944

Uncovered: 1,515,351 out of 23,391,356
Matches: 16,270,185 out of 23,391,356
Mismatches: 5,063,275 out of 23,391,356
Insertions: 542,545 out of 23,391,356
Identity over aligned base-pairs: 74.4%

Stomoxys calcitrans (Stable fly, USDA)

Uncovered: 886,319,155 out of 971,188,624
Covered: 84,869,469 out of 971,188,624

Uncovered: 1,753,294 out of 23,712,588
Matches: 16,319,855 out of 23,712,588
Mismatches: 5,132,493 out of 23,712,588
Insertions: 506,946 out of 23,712,588
Identity over aligned base-pairs: 74.3%

Block size distribution

Size range All 222,380 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,142
6.2 kb
10 bp - 100 bp
24,343
1.6 Mb
9,839
726.4 kb
100 bp - 1 kb
166,827
66.1 Mb
80,438
33.3 Mb
1 kb - 10 kb
30,055
51.8 Mb
28,243
62.7 Mb
10 kb - 100 kb
13
160.9 kb
972
20.2 Mb
100 kb - 1 Mb
20
2.8 Mb