Anopheles gambiae vs Anopheles merus LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles merus (Anopheles merus, AmerM2) 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 merus
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 133,275 alignment blocks

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

Uncovered: 24,924,687 out of 281,378,673
Covered: 256,453,986 out of 281,378,673

Uncovered: 79,826 out of 22,369,942
Matches: 20,184,031 out of 22,369,942
Mismatches: 2,067,401 out of 22,369,942
Insertions: 38,684 out of 22,369,942
Identity over aligned base-pairs: 90.6%

Anopheles merus

Uncovered: 45,510,599 out of 288,048,996
Covered: 242,538,397 out of 288,048,996

Uncovered: 43,213 out of 19,643,623
Matches: 18,792,861 out of 19,643,623
Mismatches: 764,797 out of 19,643,623
Insertions: 42,752 out of 19,643,623
Identity over aligned base-pairs: 95.9%

Block size distribution

Size range All 133,275 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,329
14.3 kb
10 bp - 100 bp
20,325
1.1 Mb
5,422
345.3 kb
100 bp - 1 kb
57,359
21.9 Mb
16,896
6.4 Mb
1 kb - 10 kb
46,712
162.5 Mb
12,637
43.8 Mb
10 kb - 100 kb
6,548
119.6 Mb
2,747
59.6 Mb
100 kb - 1 Mb
2
208.4 kb
148
65.5 Mb
1 Mb - 10 Mb
63
129.7 Mb