Glossina morsitans vs Glossina austeni LastZ Results

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Glossina morsitans (Glossina morsitans, GmorY1) and Glossina austeni (Glossina austeni, GausT1) 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: 193,541

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

Uncovered: 59,127,189 out of 366,195,856
Covered: 307,068,667 out of 366,195,856

Uncovered: 651,130 out of 20,464,474
Matches: 19,070,889 out of 20,464,474
Mismatches: 688,979 out of 20,464,474
Insertions: 53,476 out of 20,464,474

Glossina austeni

Uncovered: 65,549,419 out of 370,264,922
Covered: 304,715,503 out of 370,264,922

Uncovered: 1,400,548 out of 24,016,715
Matches: 21,582,711 out of 24,016,715
Mismatches: 892,175 out of 24,016,715
Insertions: 141,281 out of 24,016,715

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 austeni
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}