Apis mellifera (DH4) vs Solenopsis invicta LastZ results
Apis mellifera (DH4) (Apis mellifera, Amel_HAv3.1) and Solenopsis invicta (Solenopsis invicta, Si_gnH) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 102. Apis mellifera (DH4) 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 | Apis mellifera (DH4) | Solenopsis invicta |
---|---|---|
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 124,547 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Apis mellifera (DH4) |
Uncovered: 180,372,506 out of 225,250,884 |
Uncovered: 1,955,930 out of 18,346,913 |
Solenopsis invicta |
Uncovered: 350,911,381 out of 398,994,629 |
Uncovered: 5,520,809 out of 22,635,573 |
Block size distribution
Size range | All 124,547 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 488 |
3.3 kb |
|||
10 bp - 100 bp | 13,863 |
889.2 kb |
2,176 |
154.5 kb |
|
100 bp - 1 kb | 99,824 |
33.7 Mb |
16,331 |
5.7 Mb |
|
1 kb - 10 kb | 10,361 |
18.4 Mb |
4,976 |
15.1 Mb |
|
10 kb - 100 kb | 11 |
129.5 kb |
948 |
23.9 Mb |
|
100 kb - 1 Mb | 45 |
8.3 Mb |