Bombus impatiens vs Atta cephalotes LastZ Results

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Bombus impatiens (Bombus impatiens, BIMP_2.0) and Atta cephalotes (Atta cephalotes, Attacep1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Bombus impatiens 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: 174,167

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

Uncovered: 197,170,306 out of 249,185,056
Covered: 52,014,750 out of 249,185,056

Uncovered: 5,268,946 out of 22,494,304
Matches: 11,986,524 out of 22,494,304
Mismatches: 4,902,555 out of 22,494,304
Insertions: 336,279 out of 22,494,304

Atta cephalotes

Uncovered: 254,743,486 out of 317,690,795
Covered: 62,947,309 out of 317,690,795

Uncovered: 1,845,020 out of 17,986,937
Matches: 11,440,577 out of 17,986,937
Mismatches: 4,388,617 out of 17,986,937
Insertions: 312,723 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 impatiens 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}