Glossina fuscipes fuscipes vs Glossina palpalis LastZ Results

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Glossina fuscipes fuscipes (Glossina fuscipes fuscipes, GfusI1) and Glossina palpalis (Glossina palpalis gambiensis, GpapI1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1504. Glossina fuscipes fuscipes 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: 99,713

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

Uncovered: 42,505,850 out of 374,774,708
Covered: 332,268,858 out of 374,774,708

Uncovered: 978,430 out of 23,680,308
Matches: 22,461,660 out of 23,680,308
Mismatches: 201,607 out of 23,680,308
Insertions: 38,611 out of 23,680,308

Glossina palpalis gambiensis

Uncovered: 45,726,187 out of 380,104,241
Covered: 334,378,054 out of 380,104,241

Uncovered: 212,042 out of 24,050,531
Matches: 23,615,742 out of 24,050,531
Mismatches: 193,639 out of 24,050,531
Insertions: 29,108 out of 24,050,531

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 fuscipes fuscipes Glossina palpalis
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}