Glossina morsitans vs Glossina brevipalpis LastZ Results

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Glossina morsitans (Glossina morsitans, GmorY1) and Glossina brevipalpis (Glossina brevipalpis, GbreI1) 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: 99,883

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

Uncovered: 272,520,886 out of 366,195,856
Covered: 93,674,970 out of 366,195,856

Uncovered: 5,289,047 out of 20,464,474
Matches: 13,143,721 out of 20,464,474
Mismatches: 1,923,775 out of 20,464,474
Insertions: 107,931 out of 20,464,474

Glossina brevipalpis

Uncovered: 221,571,047 out of 315,360,362
Covered: 93,789,315 out of 315,360,362

Uncovered: 5,577,679 out of 20,441,857
Matches: 12,824,066 out of 20,441,857
Mismatches: 1,902,210 out of 20,441,857
Insertions: 137,902 out of 20,441,857

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 brevipalpis
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}