Anopheles gambiae vs Anopheles albimanus LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles albimanus (Anopheles albimanus, AalbS2) 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

ParameterValue
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

ParameterAnopheles gambiaeAnopheles albimanus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 114,074 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Anopheles gambiae

Uncovered: 241,097,931 out of 281,378,673
Covered: 40,280,742 out of 281,378,673

Uncovered: 2,105,026 out of 22,369,942
Matches: 14,854,514 out of 22,369,942
Mismatches: 4,845,704 out of 22,369,942
Insertions: 564,698 out of 22,369,942
Identity over aligned base-pairs: 73.3%

Anopheles albimanus

Uncovered: 136,521,984 out of 173,339,240
Covered: 36,817,256 out of 173,339,240

Uncovered: 1,630,813 out of 20,938,803
Matches: 13,904,844 out of 20,938,803
Mismatches: 4,731,264 out of 20,938,803
Insertions: 671,882 out of 20,938,803
Identity over aligned base-pairs: 72.0%

Block size distribution

Size range All 114,074 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
127
735.0 bp
10 bp - 100 bp
40,851
2.4 Mb
4,256
255.8 kb
100 bp - 1 kb
62,251
20.3 Mb
8,245
2.8 Mb
1 kb - 10 kb
10,774
20.8 Mb
3,013
8.7 Mb
10 kb - 100 kb
71
909.3 kb
678
21.2 Mb
100 kb - 1 Mb
65
10.4 Mb
1 Mb - 10 Mb
1
1.1 Mb