Glossina brevipalpis vs Glossina pallidipes LastZ Results

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Glossina brevipalpis (Glossina brevipalpis, GbreI1) and Glossina pallidipes (Glossina pallidipes, GpalI1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1504. Glossina brevipalpis 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: 103,908

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

Uncovered: 217,517,214 out of 315,360,362
Covered: 97,843,148 out of 315,360,362

Uncovered: 5,457,761 out of 20,441,857
Matches: 12,919,293 out of 20,441,857
Mismatches: 1,923,221 out of 20,441,857
Insertions: 141,582 out of 20,441,857

Glossina pallidipes

Uncovered: 259,747,019 out of 357,332,231
Covered: 97,585,212 out of 357,332,231

Uncovered: 7,173,910 out of 22,851,530
Matches: 13,475,601 out of 22,851,530
Mismatches: 2,049,837 out of 22,851,530
Insertions: 152,182 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 brevipalpis 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}