Glossina austeni vs Glossina fuscipes fuscipes LastZ Results

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Glossina austeni (Glossina austeni, GausT1) and Glossina fuscipes fuscipes (Glossina fuscipes fuscipes, GfusI1) 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: 238,906

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

Uncovered: 94,097,449 out of 370,264,922
Covered: 276,167,473 out of 370,264,922

Uncovered: 1,953,356 out of 24,032,735
Matches: 20,508,985 out of 24,032,735
Mismatches: 1,390,365 out of 24,032,735
Insertions: 180,029 out of 24,032,735

Glossina fuscipes fuscipes

Uncovered: 97,236,427 out of 374,774,708
Covered: 277,538,281 out of 374,774,708

Uncovered: 1,992,519 out of 23,680,308
Matches: 20,167,220 out of 23,680,308
Mismatches: 1,372,817 out of 23,680,308
Insertions: 147,752 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 austeni 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}