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Bombus terrestris vs Apis mellifera (DH4) LastZ results

Bombus terrestris (Bombus terrestris, Bter_1.0) and Apis mellifera (DH4) (Apis mellifera, Amel_HAv3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 102. Bombus terrestris 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

ParameterBombus terrestrisApis mellifera (DH4)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 209,914 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Bombus terrestris

Uncovered: 102,075,175 out of 248,654,244
Covered: 146,579,069 out of 248,654,244

Uncovered: 406,899 out of 18,548,448
Matches: 15,148,109 out of 18,548,448
Mismatches: 2,783,994 out of 18,548,448
Insertions: 209,446 out of 18,548,448
Identity over aligned base-pairs: 83.5%

Apis mellifera (DH4)

Uncovered: 81,691,968 out of 225,250,884
Covered: 143,558,916 out of 225,250,884

Uncovered: 234,299 out of 18,346,913
Matches: 15,003,975 out of 18,346,913
Mismatches: 2,944,801 out of 18,346,913
Insertions: 163,838 out of 18,346,913
Identity over aligned base-pairs: 82.8%

Block size distribution

Size range All 209,914 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,314
9.2 kb
10 bp - 100 bp
19,349
1.1 Mb
4,009
291.0 kb
100 bp - 1 kb
146,042
67.6 Mb
19,590
7.0 Mb
1 kb - 10 kb
42,743
89.5 Mb
3,718
8.9 Mb
10 kb - 100 kb
465
6.7 Mb
247
9.6 Mb
100 kb - 1 Mb
1
124.8 kb
185
59.6 Mb
1 Mb - 10 Mb
34
79.4 Mb