Anopheles gambiae vs Anopheles culicifacies LastZ results
Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles culicifacies (Anopheles culicifacies, AculA1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 99. Anopheles gambiae 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 | Anopheles gambiae | Anopheles culicifacies |
---|---|---|
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} |
Statistics over 182,241 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Anopheles gambiae |
Uncovered: 137,864,998 out of 281,378,673 |
Uncovered: 697,876 out of 22,369,942 |
Anopheles culicifacies |
Uncovered: 76,976,232 out of 202,998,806 |
Uncovered: 381,251 out of 20,923,336 |
Block size distribution
Size range | All 182,241 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 324 |
1.9 kb |
|||
10 bp - 100 bp | 16,015 |
999.8 kb |
2,619 |
182.2 kb |
|
100 bp - 1 kb | 110,504 |
50.0 Mb |
12,411 |
4.8 Mb |
|
1 kb - 10 kb | 55,278 |
109.0 Mb |
13,840 |
51.9 Mb |
|
10 kb - 100 kb | 120 |
1.5 Mb |
4,482 |
99.8 Mb |
|
100 kb - 1 Mb | 37 |
4.8 Mb |