Lucilia cuprina vs Glossina fuscipes fuscipes LastZ Results

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Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Glossina fuscipes fuscipes (Glossina fuscipes fuscipes, GfusI1) 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: 88,549

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

Uncovered: 398,707,480 out of 434,128,924
Covered: 35,421,444 out of 434,128,924

Uncovered: 4,704,493 out of 22,222,068
Matches: 12,129,470 out of 22,222,068
Mismatches: 4,776,351 out of 22,222,068
Insertions: 611,754 out of 22,222,068

Glossina fuscipes fuscipes

Uncovered: 337,273,557 out of 374,774,708
Covered: 37,501,151 out of 374,774,708

Uncovered: 5,317,030 out of 23,696,776
Matches: 12,838,038 out of 23,696,776
Mismatches: 5,082,811 out of 23,696,776
Insertions: 458,897 out of 23,696,776

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 fuscipes fuscipes
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}