Glossina pallidipes vs Glossina palpalis LastZ Results

Back to all analyses

Glossina pallidipes (Glossina pallidipes, GpalI1) and Glossina palpalis (Glossina palpalis gambiensis, GpapI1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1504. Glossina pallidipes 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: 242,729

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

Uncovered: 86,514,993 out of 357,332,231
Covered: 270,817,238 out of 357,332,231

Uncovered: 1,568,647 out of 22,851,530
Matches: 19,804,282 out of 22,851,530
Mismatches: 1,325,443 out of 22,851,530
Insertions: 153,158 out of 22,851,530

Glossina palpalis gambiensis

Uncovered: 104,017,155 out of 380,104,241
Covered: 276,087,086 out of 380,104,241

Uncovered: 1,298,195 out of 24,050,531
Matches: 21,221,233 out of 24,050,531
Mismatches: 1,388,284 out of 24,050,531
Insertions: 142,819 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 pallidipes 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}