Glossina morsitans vs Glossina fuscipes fuscipes LastZ Results

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Glossina morsitans (Glossina morsitans, GmorY1) and Glossina fuscipes fuscipes (Glossina fuscipes fuscipes, GfusI1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1504. Glossina morsitans 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: 247,483

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

Uncovered: 82,789,530 out of 366,195,856
Covered: 283,406,326 out of 366,195,856

Uncovered: 815,135 out of 20,464,474
Matches: 18,498,754 out of 20,464,474
Mismatches: 1,074,264 out of 20,464,474
Insertions: 76,321 out of 20,464,474

Glossina fuscipes fuscipes

Uncovered: 91,415,647 out of 374,774,708
Covered: 283,359,061 out of 374,774,708

Uncovered: 1,969,371 out of 23,680,308
Matches: 20,242,457 out of 23,680,308
Mismatches: 1,319,369 out of 23,680,308
Insertions: 149,111 out of 23,680,308

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 morsitans Glossina fuscipes fuscipes
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}