Apis mellifera vs Bombus impatiens LastZ Results

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Apis mellifera (Apis mellifera, Amel_4.5) and Bombus impatiens (Bombus impatiens, BIMP_2.0) 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: 243,609

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

Uncovered: 96,604,329 out of 250,270,657
Covered: 153,666,328 out of 250,270,657

Uncovered: 701,086 out of 19,369,619
Matches: 15,509,287 out of 19,369,619
Mismatches: 2,972,591 out of 19,369,619
Insertions: 186,655 out of 19,369,619

Bombus impatiens

Uncovered: 97,847,310 out of 249,185,056
Covered: 151,337,746 out of 249,185,056

Uncovered: 3,699,702 out of 22,494,304
Matches: 14,840,814 out of 22,494,304
Mismatches: 3,720,072 out of 22,494,304
Insertions: 233,716 out of 22,494,304

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 Bombus impatiens
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}