Glossina austeni vs Glossina brevipalpis LastZ Results

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Glossina austeni (Glossina austeni, GausT1) and Glossina brevipalpis (Glossina brevipalpis, GbreI1) 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: 99,814

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

Uncovered: 278,346,056 out of 370,264,922
Covered: 91,918,866 out of 370,264,922

Uncovered: 8,028,907 out of 24,032,735
Matches: 13,741,133 out of 24,032,735
Mismatches: 2,098,459 out of 24,032,735
Insertions: 164,236 out of 24,032,735

Glossina brevipalpis

Uncovered: 223,875,276 out of 315,360,362
Covered: 91,485,086 out of 315,360,362

Uncovered: 5,686,328 out of 20,441,857
Matches: 12,712,598 out of 20,441,857
Mismatches: 1,908,016 out of 20,441,857
Insertions: 134,915 out of 20,441,857

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 --identity=80..100 --matchcount=1000

Chunking parameters

Glossina austeni Glossina brevipalpis
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}