Lucilia cuprina vs Glossina morsitans LastZ Results

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Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Glossina morsitans (Glossina morsitans morsitans, GmorY1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Lucilia cuprina 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: 85,544

Genome coverage (bp) Coding exon coverage (bp)
Lucilia cuprina

Uncovered: 399,861,894 out of 434,128,924
Covered: 34,267,030 out of 434,128,924

Uncovered: 4,752,066 out of 22,222,068
Matches: 12,143,741 out of 22,222,068
Mismatches: 4,714,563 out of 22,222,068
Insertions: 611,698 out of 22,222,068

Glossina morsitans morsitans

Uncovered: 330,766,181 out of 366,195,856
Covered: 35,429,675 out of 366,195,856

Uncovered: 2,707,863 out of 20,527,791
Matches: 12,518,261 out of 20,527,791
Mismatches: 4,863,820 out of 20,527,791
Insertions: 437,847 out of 20,527,791

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

Lucilia cuprina Glossina morsitans
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}