Anopheles gambiae vs Anopheles dirus LastZ results
Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles dirus (Anopheles dirus, AdirW1) 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 dirus |
---|---|---|
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 200,021 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Anopheles gambiae |
Uncovered: 161,359,360 out of 281,378,673 |
Uncovered: 703,890 out of 22,369,942 |
Anopheles dirus |
Uncovered: 112,112,188 out of 216,307,690 |
Uncovered: 581,333 out of 21,096,405 |
Block size distribution
Size range | All 200,021 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 351 |
2.2 kb |
|||
10 bp - 100 bp | 25,088 |
1.5 Mb |
2,039 |
136.8 kb |
|
100 bp - 1 kb | 134,054 |
57.2 Mb |
9,486 |
3.7 Mb |
|
1 kb - 10 kb | 40,384 |
73.0 Mb |
4,744 |
12.8 Mb |
|
10 kb - 100 kb | 144 |
2.2 Mb |
544 |
14.6 Mb |
|
100 kb - 1 Mb | 162 |
55.9 Mb |
|||
1 Mb - 10 Mb | 24 |
46.7 Mb |