Anopheles gambiae vs Anopheles sinensis LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles sinensis (Anopheles sinensis, AsinS2) 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 sinensis
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 156,256 alignment blocks

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

Uncovered: 205,597,991 out of 281,378,673
Covered: 75,780,682 out of 281,378,673

Uncovered: 1,759,799 out of 22,369,942
Matches: 13,289,657 out of 22,369,942
Mismatches: 6,852,772 out of 22,369,942
Insertions: 467,714 out of 22,369,942
Identity over aligned base-pairs: 64.5%

Anopheles sinensis

Uncovered: 300,162,221 out of 375,763,635
Covered: 75,601,414 out of 375,763,635

Uncovered: 1,212,271 out of 17,380,207
Matches: 12,047,944 out of 17,380,207
Mismatches: 3,699,458 out of 17,380,207
Insertions: 420,534 out of 17,380,207
Identity over aligned base-pairs: 74.5%

Block size distribution

Size range All 156,256 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
198
1.1 kb
10 bp - 100 bp
37,951
2.3 Mb
5,328
341.8 kb
100 bp - 1 kb
100,581
35.8 Mb
16,791
6.6 Mb
1 kb - 10 kb
16,629
33.7 Mb
8,002
22.9 Mb
10 kb - 100 kb
897
23.3 Mb
1,278
43.0 Mb
100 kb - 1 Mb
115
22.3 Mb