Glossina fuscipes fuscipes vs Musca domestica LastZ Results

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Glossina fuscipes fuscipes (Glossina fuscipes fuscipes, GfusI1) and Musca domestica (Musca domestica, MdomA1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1504. Glossina fuscipes fuscipes 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: 79,341

Genome coverage (bp) Coding exon coverage (bp)
Glossina fuscipes fuscipes

Uncovered: 346,606,954 out of 374,774,708
Covered: 28,167,754 out of 374,774,708

Uncovered: 6,497,344 out of 23,680,308
Matches: 11,908,606 out of 23,680,308
Mismatches: 4,860,913 out of 23,680,308
Insertions: 413,445 out of 23,680,308

Musca domestica

Uncovered: 720,769,562 out of 750,403,944
Covered: 29,634,382 out of 750,403,944

Uncovered: 4,755,661 out of 22,967,770
Matches: 12,467,817 out of 22,967,770
Mismatches: 5,116,456 out of 22,967,770
Insertions: 627,836 out of 22,967,770

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

Glossina fuscipes fuscipes Musca domestica
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}