Glossina morsitans vs Glossina pallidipes LastZ Results

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Glossina morsitans (Glossina morsitans, GmorY1) and Glossina pallidipes (Glossina pallidipes, GpalI1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1504. Glossina morsitans 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: 163,821

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

Uncovered: 41,367,954 out of 366,195,856
Covered: 324,827,902 out of 366,195,856

Uncovered: 529,961 out of 20,464,474
Matches: 19,390,880 out of 20,464,474
Mismatches: 499,366 out of 20,464,474
Insertions: 44,267 out of 20,464,474

Glossina pallidipes

Uncovered: 38,250,517 out of 357,332,231
Covered: 319,081,714 out of 357,332,231

Uncovered: 793,234 out of 22,851,530
Matches: 21,325,685 out of 22,851,530
Mismatches: 646,255 out of 22,851,530
Insertions: 86,356 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 morsitans 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}