Glossina austeni vs Glossina pallidipes LastZ Results

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Glossina austeni (Glossina austeni, GausT1) and Glossina pallidipes (Glossina pallidipes, GpalI1) 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: 178,007

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

Uncovered: 64,631,104 out of 370,264,922
Covered: 305,633,818 out of 370,264,922

Uncovered: 1,505,339 out of 24,032,735
Matches: 21,489,076 out of 24,032,735
Mismatches: 900,120 out of 24,032,735
Insertions: 138,200 out of 24,032,735

Glossina pallidipes

Uncovered: 53,884,685 out of 357,332,231
Covered: 303,447,546 out of 357,332,231

Uncovered: 954,582 out of 22,851,530
Matches: 20,900,656 out of 22,851,530
Mismatches: 889,982 out of 22,851,530
Insertions: 106,310 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 austeni 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}