Anopheles gambiae vs Anopheles quadriannulatus LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles quadriannulatus (Anopheles quadriannulatus, AquaS1) 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 quadriannulatus
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 123,720 alignment blocks

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

Uncovered: 25,247,816 out of 281,378,673
Covered: 256,130,857 out of 281,378,673

Uncovered: 97,438 out of 22,369,942
Matches: 19,896,429 out of 22,369,942
Mismatches: 2,346,058 out of 22,369,942
Insertions: 30,017 out of 22,369,942
Identity over aligned base-pairs: 89.3%

Anopheles quadriannulatus

Uncovered: 30,100,939 out of 283,828,998
Covered: 253,728,059 out of 283,828,998

Uncovered: 61,626 out of 21,196,160
Matches: 20,362,538 out of 21,196,160
Mismatches: 737,823 out of 21,196,160
Insertions: 34,173 out of 21,196,160
Identity over aligned base-pairs: 96.3%

Block size distribution

Size range All 123,720 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,807
11.1 kb
10 bp - 100 bp
16,570
943.5 kb
4,824
308.2 kb
100 bp - 1 kb
51,627
20.3 Mb
17,182
6.7 Mb
1 kb - 10 kb
46,180
167.3 Mb
14,210
54.3 Mb
10 kb - 100 kb
7,527
123.0 Mb
3,767
61.1 Mb
100 kb - 1 Mb
9
1.1 Mb
175
69.5 Mb
1 Mb - 10 Mb
61
120.9 Mb