Glossina pallidipes vs Musca domestica LastZ Results

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Glossina pallidipes (Glossina pallidipes, GpalI1) and Musca domestica (Musca domestica, MdomA1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1504. Glossina pallidipes 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: 79,648

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

Uncovered: 329,521,265 out of 357,332,231
Covered: 27,810,966 out of 357,332,231

Uncovered: 6,156,725 out of 22,851,530
Matches: 11,583,616 out of 22,851,530
Mismatches: 4,709,492 out of 22,851,530
Insertions: 401,697 out of 22,851,530

Musca domestica

Uncovered: 719,968,453 out of 750,403,944
Covered: 30,435,491 out of 750,403,944

Uncovered: 4,728,475 out of 22,967,770
Matches: 12,491,737 out of 22,967,770
Mismatches: 5,120,095 out of 22,967,770
Insertions: 627,463 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 pallidipes 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}