Glossina morsitans vs Glossina palpalis LastZ Results

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Glossina morsitans (Glossina morsitans, GmorY1) and Glossina palpalis (Glossina palpalis gambiensis, GpapI1) 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: 251,475

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

Uncovered: 94,348,194 out of 366,195,856
Covered: 271,847,662 out of 366,195,856

Uncovered: 1,047,369 out of 20,464,474
Matches: 18,272,189 out of 20,464,474
Mismatches: 1,069,159 out of 20,464,474
Insertions: 75,757 out of 20,464,474

Glossina palpalis gambiensis

Uncovered: 105,873,827 out of 380,104,241
Covered: 274,230,414 out of 380,104,241

Uncovered: 1,461,685 out of 24,050,531
Matches: 21,090,075 out of 24,050,531
Mismatches: 1,357,829 out of 24,050,531
Insertions: 140,942 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 morsitans 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}