Apis mellifera vs Bombus terrestris LastZ Results

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Apis mellifera (Apis mellifera, Amel_4.5) and Bombus terrestris (Bombus terrestris, Bter_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Apis mellifera was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 230,886

Genome coverage (bp) Coding exon coverage (bp)
Apis mellifera

Uncovered: 95,668,743 out of 250,270,657
Covered: 154,601,914 out of 250,270,657

Uncovered: 757,031 out of 19,369,619
Matches: 15,372,270 out of 19,369,619
Mismatches: 3,055,147 out of 19,369,619
Insertions: 185,171 out of 19,369,619

Bombus terrestris

Uncovered: 96,851,403 out of 248,654,244
Covered: 151,802,841 out of 248,654,244

Uncovered: 436,825 out of 18,548,448
Matches: 14,593,926 out of 18,548,448
Mismatches: 3,308,670 out of 18,548,448
Insertions: 209,027 out of 18,548,448

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Apis mellifera Bombus terrestris
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}