Anopheles gambiae vs Anopheles melas LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles melas (Anopheles melas, AmelC2) 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 melas
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 144,552 alignment blocks

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

Uncovered: 50,065,266 out of 281,378,673
Covered: 231,313,407 out of 281,378,673

Uncovered: 354,119 out of 22,369,942
Matches: 20,959,114 out of 22,369,942
Mismatches: 1,009,582 out of 22,369,942
Insertions: 47,127 out of 22,369,942
Identity over aligned base-pairs: 95.2%

Anopheles melas

Uncovered: 15,394,707 out of 224,162,116
Covered: 208,767,409 out of 224,162,116

Uncovered: 134,997 out of 20,575,065
Matches: 19,608,999 out of 20,575,065
Mismatches: 786,122 out of 20,575,065
Insertions: 44,947 out of 20,575,065
Identity over aligned base-pairs: 95.9%

Block size distribution

Size range All 144,552 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,866
11.5 kb
10 bp - 100 bp
19,724
1.2 Mb
6,897
445.0 kb
100 bp - 1 kb
62,493
24.3 Mb
23,518
9.0 Mb
1 kb - 10 kb
56,983
184.4 Mb
26,160
97.9 Mb
10 kb - 100 kb
3,486
52.3 Mb
7,560
152.7 Mb
100 kb - 1 Mb
18
2.1 Mb