Bombus terrestris vs Solenopsis invicta LastZ Results

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Bombus terrestris (Bombus terrestris, Bter_1.0) and Solenopsis invicta (Solenopsis invicta, Si_gnG) 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: 165,576

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

Uncovered: 194,856,261 out of 248,654,244
Covered: 53,797,983 out of 248,654,244

Uncovered: 2,000,306 out of 18,548,448
Matches: 11,564,536 out of 18,548,448
Mismatches: 4,707,259 out of 18,548,448
Insertions: 276,347 out of 18,548,448

Solenopsis invicta

Uncovered: 334,612,861 out of 396,024,718
Covered: 61,411,857 out of 396,024,718

Uncovered: 4,375,415 out of 21,684,807
Matches: 12,124,062 out of 21,684,807
Mismatches: 4,831,144 out of 21,684,807
Insertions: 354,186 out of 21,684,807

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 Solenopsis invicta
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}