Glossina brevipalpis vs Musca domestica LastZ Results

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Glossina brevipalpis (Glossina brevipalpis, GbreI1) and Musca domestica (Musca domestica, MdomA1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1504. Glossina brevipalpis 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: 68,621

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

Uncovered: 289,993,278 out of 315,360,362
Covered: 25,367,084 out of 315,360,362

Uncovered: 4,280,569 out of 20,441,857
Matches: 11,244,644 out of 20,441,857
Mismatches: 4,532,861 out of 20,441,857
Insertions: 383,783 out of 20,441,857

Musca domestica

Uncovered: 721,229,018 out of 750,403,944
Covered: 29,174,926 out of 750,403,944

Uncovered: 4,787,675 out of 22,967,770
Matches: 12,461,883 out of 22,967,770
Mismatches: 5,089,929 out of 22,967,770
Insertions: 628,283 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 brevipalpis 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}