Apis mellifera vs Solenopsis invicta LastZ Results

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Apis mellifera (Apis mellifera, Amel_4.5) and Solenopsis invicta (Solenopsis invicta, Si_gnG) 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: 133,978

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

Uncovered: 202,377,388 out of 250,270,657
Covered: 47,893,269 out of 250,270,657

Uncovered: 2,790,546 out of 19,369,619
Matches: 11,583,108 out of 19,369,619
Mismatches: 4,702,305 out of 19,369,619
Insertions: 293,660 out of 19,369,619

Solenopsis invicta

Uncovered: 343,362,685 out of 396,024,718
Covered: 52,662,033 out of 396,024,718

Uncovered: 4,810,068 out of 21,684,807
Matches: 11,786,891 out of 21,684,807
Mismatches: 4,726,415 out of 21,684,807
Insertions: 361,433 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

Apis mellifera 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}