Anopheles gambiae vs Anopheles farauti LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles farauti (Anopheles farauti, AfarF2) 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 farauti
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 193,123 alignment blocks

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

Uncovered: 173,155,461 out of 281,378,673
Covered: 108,223,212 out of 281,378,673

Uncovered: 812,563 out of 22,369,942
Matches: 16,659,824 out of 22,369,942
Mismatches: 4,360,080 out of 22,369,942
Insertions: 537,475 out of 22,369,942
Identity over aligned base-pairs: 77.3%

Anopheles farauti

Uncovered: 88,527,113 out of 183,103,254
Covered: 94,576,141 out of 183,103,254

Uncovered: 563,877 out of 20,347,302
Matches: 15,245,802 out of 20,347,302
Mismatches: 4,114,434 out of 20,347,302
Insertions: 423,189 out of 20,347,302
Identity over aligned base-pairs: 77.1%

Block size distribution

Size range All 193,123 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
271
1.7 kb
10 bp - 100 bp
27,276
1.7 Mb
1,679
109.9 kb
100 bp - 1 kb
130,279
54.3 Mb
6,628
2.7 Mb
1 kb - 10 kb
35,217
62.5 Mb
3,623
9.4 Mb
10 kb - 100 kb
80
1.0 Mb
445
12.4 Mb
100 kb - 1 Mb
168
55.2 Mb
1 Mb - 10 Mb
20
39.7 Mb