Anopheles gambiae vs Anopheles funestus LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles funestus (Anopheles funestus, AfunF3) 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 funestus
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 181,005 alignment blocks

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

Uncovered: 136,786,666 out of 281,378,673
Covered: 144,592,007 out of 281,378,673

Uncovered: 1,124,843 out of 22,369,942
Matches: 16,769,606 out of 22,369,942
Mismatches: 4,038,000 out of 22,369,942
Insertions: 437,493 out of 22,369,942
Identity over aligned base-pairs: 78.9%

Anopheles funestus

Uncovered: 76,528,212 out of 210,989,154
Covered: 134,460,942 out of 210,989,154

Uncovered: 452,169 out of 22,083,846
Matches: 16,877,745 out of 22,083,846
Mismatches: 4,459,111 out of 22,083,846
Insertions: 294,821 out of 22,083,846
Identity over aligned base-pairs: 78.0%

Block size distribution

Size range All 181,005 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
482
2.9 kb
10 bp - 100 bp
16,878
1.0 Mb
3,341
230.2 kb
100 bp - 1 kb
105,741
47.2 Mb
13,149
4.7 Mb
1 kb - 10 kb
57,724
118.4 Mb
5,561
14.6 Mb
10 kb - 100 kb
180
2.3 Mb
527
13.7 Mb
100 kb - 1 Mb
129
41.7 Mb
1 Mb - 10 Mb
23
61.2 Mb
10 Mb - 100 Mb
3
32.8 Mb