Atta cephalotes vs Solenopsis invicta LastZ Results

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Atta cephalotes (Atta cephalotes, Attacep1.0) and Solenopsis invicta (Solenopsis invicta, Si_gnG) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Atta cephalotes 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: 650,370

Genome coverage (bp) Coding exon coverage (bp)
Atta cephalotes

Uncovered: 43,436,404 out of 317,690,795
Covered: 274,254,391 out of 317,690,795

Uncovered: 111,677 out of 17,986,937
Matches: 14,462,005 out of 17,986,937
Mismatches: 3,271,061 out of 17,986,937
Insertions: 142,194 out of 17,986,937

Solenopsis invicta

Uncovered: 97,355,400 out of 396,024,718
Covered: 298,669,318 out of 396,024,718

Uncovered: 1,357,772 out of 21,684,807
Matches: 16,235,119 out of 21,684,807
Mismatches: 3,819,415 out of 21,684,807
Insertions: 272,501 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

Atta cephalotes 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}