Glossina austeni vs Glossina palpalis LastZ Results

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Glossina austeni (Glossina austeni, GausT1) and Glossina palpalis (Glossina palpalis gambiensis, GpapI1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1504. Glossina austeni 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: 243,587

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

Uncovered: 104,295,183 out of 370,264,922
Covered: 265,969,739 out of 370,264,922

Uncovered: 2,211,020 out of 24,032,735
Matches: 20,260,128 out of 24,032,735
Mismatches: 1,382,191 out of 24,032,735
Insertions: 179,396 out of 24,032,735

Glossina palpalis gambiensis

Uncovered: 110,693,078 out of 380,104,241
Covered: 269,411,163 out of 380,104,241

Uncovered: 1,405,926 out of 24,050,531
Matches: 21,080,075 out of 24,050,531
Mismatches: 1,424,976 out of 24,050,531
Insertions: 139,554 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 austeni 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}