Anopheles gambiae vs Anopheles maculatus LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles maculatus (Anopheles maculatus, AmacM1) 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 maculatus
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 140,202 alignment blocks

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

Uncovered: 184,386,315 out of 281,378,673
Covered: 96,992,358 out of 281,378,673

Uncovered: 4,072,648 out of 22,369,942
Matches: 14,223,668 out of 22,369,942
Mismatches: 3,714,175 out of 22,369,942
Insertions: 359,451 out of 22,369,942
Identity over aligned base-pairs: 77.7%

Anopheles maculatus

Uncovered: 57,589,048 out of 141,894,015
Covered: 84,304,967 out of 141,894,015

Uncovered: 592,576 out of 16,388,885
Matches: 12,510,800 out of 16,388,885
Mismatches: 3,011,420 out of 16,388,885
Insertions: 274,089 out of 16,388,885
Identity over aligned base-pairs: 79.2%

Block size distribution

Size range All 140,202 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
162
985.0 bp
10 bp - 100 bp
11,885
760.1 kb
2,342
165.9 kb
100 bp - 1 kb
89,936
40.8 Mb
19,162
9.5 Mb
1 kb - 10 kb
38,214
65.4 Mb
37,478
92.4 Mb
10 kb - 100 kb
5
59.2 kb
392
5.0 Mb