Anopheles gambiae vs Anopheles epiroticus LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles epiroticus (Anopheles epiroticus, AepiE1) 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 epiroticus
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 142,670 alignment blocks

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

Uncovered: 106,055,782 out of 281,378,673
Covered: 175,322,891 out of 281,378,673

Uncovered: 347,153 out of 22,369,942
Matches: 18,026,689 out of 22,369,942
Mismatches: 3,611,402 out of 22,369,942
Insertions: 384,698 out of 22,369,942
Identity over aligned base-pairs: 81.9%

Anopheles epiroticus

Uncovered: 70,921,218 out of 223,486,714
Covered: 152,565,496 out of 223,486,714

Uncovered: 202,104 out of 20,285,978
Matches: 16,476,448 out of 20,285,978
Mismatches: 3,353,680 out of 20,285,978
Insertions: 253,746 out of 20,285,978
Identity over aligned base-pairs: 82.0%

Block size distribution

Size range All 142,670 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
428
2.8 kb
10 bp - 100 bp
10,899
669.9 kb
2,845
203.0 kb
100 bp - 1 kb
67,257
31.0 Mb
11,317
4.1 Mb
1 kb - 10 kb
63,316
152.4 Mb
6,306
18.1 Mb
10 kb - 100 kb
770
10.5 Mb
1,030
34.7 Mb
100 kb - 1 Mb
437
115.9 Mb
1 Mb - 10 Mb
15
21.7 Mb