Glossina austeni vs Musca domestica LastZ Results

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Glossina austeni (Glossina austeni, GausT1) and Musca domestica (Musca domestica, MdomA1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1504. Glossina austeni 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: 79,317

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

Uncovered: 342,522,179 out of 370,264,922
Covered: 27,742,743 out of 370,264,922

Uncovered: 6,698,614 out of 24,032,735
Matches: 12,012,609 out of 24,032,735
Mismatches: 4,898,201 out of 24,032,735
Insertions: 423,311 out of 24,032,735

Musca domestica

Uncovered: 720,068,630 out of 750,403,944
Covered: 30,335,314 out of 750,403,944

Uncovered: 4,806,033 out of 22,967,770
Matches: 12,438,024 out of 22,967,770
Mismatches: 5,100,584 out of 22,967,770
Insertions: 623,129 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 austeni 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}