Glossina austeni vs Glossina pallidipes LastZ Results
Back to all analyses
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 |
Uncovered: 1,505,339 out of 24,032,735 |
Glossina pallidipes |
Uncovered: 53,884,685 out of 357,332,231 |
Uncovered: 954,582 out of 22,851,530 |
Configuration parameters
Parameter | Value |
---|---|
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} |