Glossina brevipalpis vs Glossina fuscipes fuscipes LastZ Results

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Glossina brevipalpis (Glossina brevipalpis, GbreI1) and Glossina fuscipes fuscipes (Glossina fuscipes fuscipes, GfusI1) 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: 101,736

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

Uncovered: 221,765,379 out of 315,360,362
Covered: 93,594,983 out of 315,360,362

Uncovered: 5,744,893 out of 20,441,857
Matches: 12,648,912 out of 20,441,857
Mismatches: 1,910,197 out of 20,441,857
Insertions: 137,855 out of 20,441,857

Glossina fuscipes fuscipes

Uncovered: 280,173,703 out of 374,774,708
Covered: 94,601,005 out of 374,774,708

Uncovered: 8,164,004 out of 23,680,308
Matches: 13,319,833 out of 23,680,308
Mismatches: 2,046,912 out of 23,680,308
Insertions: 149,559 out of 23,680,308

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 fuscipes fuscipes
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}