Glossina fuscipes fuscipes vs Glossina pallidipes LastZ Results

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Glossina fuscipes fuscipes (Glossina fuscipes fuscipes, GfusI1) and Glossina pallidipes (Glossina pallidipes, GpalI1) 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: 237,671

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

Uncovered: 89,528,497 out of 374,774,708
Covered: 285,246,211 out of 374,774,708

Uncovered: 1,819,816 out of 23,680,308
Matches: 20,362,657 out of 23,680,308
Mismatches: 1,345,425 out of 23,680,308
Insertions: 152,410 out of 23,680,308

Glossina pallidipes

Uncovered: 75,401,487 out of 357,332,231
Covered: 281,930,744 out of 357,332,231

Uncovered: 1,276,134 out of 22,851,530
Matches: 20,079,560 out of 22,851,530
Mismatches: 1,339,584 out of 22,851,530
Insertions: 156,252 out of 22,851,530

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 pallidipes
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}