Bombus terrestris vs Atta cephalotes LastZ Results

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Bombus terrestris (Bombus terrestris, Bter_1.0) and Atta cephalotes (Atta cephalotes, Attacep1.0) 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: 150,438

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

Uncovered: 198,478,259 out of 248,654,244
Covered: 50,175,985 out of 248,654,244

Uncovered: 2,131,260 out of 18,548,448
Matches: 11,570,078 out of 18,548,448
Mismatches: 4,552,761 out of 18,548,448
Insertions: 294,349 out of 18,548,448

Atta cephalotes

Uncovered: 257,563,860 out of 317,690,795
Covered: 60,126,935 out of 317,690,795

Uncovered: 1,824,938 out of 17,986,937
Matches: 11,426,178 out of 17,986,937
Mismatches: 4,421,879 out of 17,986,937
Insertions: 313,942 out of 17,986,937

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 Atta cephalotes
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}