Bombus terrestris vs Bombus impatiens LastZ Results

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Bombus terrestris (Bombus terrestris, Bter_1.0) and Bombus impatiens (Bombus impatiens, BIMP_2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Bombus terrestris 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: 148,195

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

Uncovered: 5,940,729 out of 248,654,244
Covered: 242,713,515 out of 248,654,244

Uncovered: 33,252 out of 18,548,448
Matches: 17,894,539 out of 18,548,448
Mismatches: 602,081 out of 18,548,448
Insertions: 18,576 out of 18,548,448

Bombus impatiens

Uncovered: 6,968,016 out of 249,185,056
Covered: 242,217,040 out of 249,185,056

Uncovered: 1,699,966 out of 22,494,304
Matches: 19,103,122 out of 22,494,304
Mismatches: 1,625,923 out of 22,494,304
Insertions: 65,293 out of 22,494,304

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

Bombus terrestris Bombus impatiens
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}