Glossina brevipalpis vs Glossina palpalis LastZ Results

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Glossina brevipalpis (Glossina brevipalpis, GbreI1) and Glossina palpalis (Glossina palpalis gambiensis, GpapI1) 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: 96,271

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

Uncovered: 228,750,005 out of 315,360,362
Covered: 86,610,357 out of 315,360,362

Uncovered: 6,092,490 out of 20,441,857
Matches: 12,354,735 out of 20,441,857
Mismatches: 1,861,930 out of 20,441,857
Insertions: 132,702 out of 20,441,857

Glossina palpalis gambiensis

Uncovered: 291,478,792 out of 380,104,241
Covered: 88,625,449 out of 380,104,241

Uncovered: 7,878,049 out of 24,050,531
Matches: 13,904,178 out of 24,050,531
Mismatches: 2,120,726 out of 24,050,531
Insertions: 147,578 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 brevipalpis 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}