Glossina morsitans vs Musca domestica LastZ Results

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Glossina morsitans (Glossina morsitans, GmorY1) and Musca domestica (Musca domestica, MdomA1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1504. Glossina morsitans 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: 93,302

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

Uncovered: 341,045,204 out of 366,195,856
Covered: 25,150,652 out of 366,195,856

Uncovered: 4,723,937 out of 20,464,474
Matches: 10,937,539 out of 20,464,474
Mismatches: 4,431,864 out of 20,464,474
Insertions: 371,134 out of 20,464,474

Musca domestica

Uncovered: 723,367,430 out of 750,403,944
Covered: 27,036,514 out of 750,403,944

Uncovered: 5,813,229 out of 22,967,770
Matches: 11,740,557 out of 22,967,770
Mismatches: 4,829,556 out of 22,967,770
Insertions: 584,428 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 morsitans 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}