Bombus impatiens vs Solenopsis invicta LastZ Results

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Bombus impatiens (Bombus impatiens, BIMP_2.0) and Solenopsis invicta (Solenopsis invicta, Si_gnG) 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: 182,053

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

Uncovered: 190,685,580 out of 249,185,056
Covered: 58,499,476 out of 249,185,056

Uncovered: 4,683,470 out of 22,494,304
Matches: 12,146,751 out of 22,494,304
Mismatches: 5,347,611 out of 22,494,304
Insertions: 316,472 out of 22,494,304

Solenopsis invicta

Uncovered: 334,009,862 out of 396,024,718
Covered: 62,014,856 out of 396,024,718

Uncovered: 4,353,691 out of 21,684,807
Matches: 12,134,234 out of 21,684,807
Mismatches: 4,842,218 out of 21,684,807
Insertions: 354,664 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 impatiens 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}