Anopheles gambiae vs Anopheles arabiensis LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles arabiensis (Anopheles arabiensis, AaraD1) 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 arabiensis
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 105,829 alignment blocks

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

Uncovered: 25,370,195 out of 281,378,673
Covered: 256,008,478 out of 281,378,673

Uncovered: 89,969 out of 22,369,942
Matches: 21,166,434 out of 22,369,942
Mismatches: 1,086,946 out of 22,369,942
Insertions: 26,593 out of 22,369,942
Identity over aligned base-pairs: 95.0%

Anopheles arabiensis

Uncovered: 20,344,042 out of 246,567,867
Covered: 226,223,825 out of 246,567,867

Uncovered: 78,835 out of 21,731,225
Matches: 20,864,666 out of 21,731,225
Mismatches: 759,189 out of 21,731,225
Insertions: 28,535 out of 21,731,225
Identity over aligned base-pairs: 96.4%

Block size distribution

Size range All 105,829 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,629
10.1 kb
10 bp - 100 bp
15,101
846.0 kb
4,341
276.9 kb
100 bp - 1 kb
43,466
17.0 Mb
14,219
5.5 Mb
1 kb - 10 kb
38,999
140.2 Mb
11,295
39.4 Mb
10 kb - 100 kb
6,614
122.2 Mb
2,176
39.4 Mb
100 kb - 1 Mb
20
2.6 Mb
43
11.4 Mb
1 Mb - 10 Mb
47
176.4 Mb
10 Mb - 100 Mb
1
10.4 Mb