Glossina palpalis vs Musca domestica LastZ Results

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Glossina palpalis (Glossina palpalis gambiensis, GpapI1) and Musca domestica (Musca domestica, MdomA1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. Glossina palpalis 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: 77,122

Genome coverage (bp) Coding exon coverage (bp)
Glossina palpalis gambiensis

Uncovered: 351,792,888 out of 380,104,241
Covered: 28,311,353 out of 380,104,241

Uncovered: 6,121,915 out of 24,050,531
Matches: 12,422,574 out of 24,050,531
Mismatches: 5,068,654 out of 24,050,531
Insertions: 437,388 out of 24,050,531

Musca domestica

Uncovered: 721,622,655 out of 750,403,944
Covered: 28,781,289 out of 750,403,944

Uncovered: 4,897,484 out of 22,967,770
Matches: 12,367,004 out of 22,967,770
Mismatches: 5,079,162 out of 22,967,770
Insertions: 624,120 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 palpalis 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}