Bombus terrestris vs Apis mellifera (DH4) LastZ results
Bombus terrestris (Bombus terrestris, Bter_1.0) and Apis mellifera (DH4) (Apis mellifera, Amel_HAv3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 102. Bombus terrestris was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
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 |
Chunking parameters
Parameter | Bombus terrestris | Apis mellifera (DH4) |
---|---|---|
Chunk size | 10,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 10,100,000 | 10,100,000 |
Masking options |
Statistics over 209,914 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Bombus terrestris |
Uncovered: 102,075,175 out of 248,654,244 |
Uncovered: 406,899 out of 18,548,448 |
Apis mellifera (DH4) |
Uncovered: 81,691,968 out of 225,250,884 |
Uncovered: 234,299 out of 18,346,913 |
Block size distribution
Size range | All 209,914 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 1,314 |
9.2 kb |
|||
10 bp - 100 bp | 19,349 |
1.1 Mb |
4,009 |
291.0 kb |
|
100 bp - 1 kb | 146,042 |
67.6 Mb |
19,590 |
7.0 Mb |
|
1 kb - 10 kb | 42,743 |
89.5 Mb |
3,718 |
8.9 Mb |
|
10 kb - 100 kb | 465 |
6.7 Mb |
247 |
9.6 Mb |
|
100 kb - 1 Mb | 1 |
124.8 kb |
185 |
59.6 Mb |
|
1 Mb - 10 Mb | 34 |
79.4 Mb |