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Anopheles gambiae vs Anopheles dirus LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles dirus (Anopheles dirus, AdirW1) 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 dirus
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 200,021 alignment blocks

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

Uncovered: 161,359,360 out of 281,378,673
Covered: 120,019,313 out of 281,378,673

Uncovered: 703,890 out of 22,369,942
Matches: 16,875,145 out of 22,369,942
Mismatches: 4,264,630 out of 22,369,942
Insertions: 526,277 out of 22,369,942
Identity over aligned base-pairs: 77.9%

Anopheles dirus

Uncovered: 112,112,188 out of 216,307,690
Covered: 104,195,502 out of 216,307,690

Uncovered: 581,333 out of 21,096,405
Matches: 15,925,254 out of 21,096,405
Mismatches: 4,184,656 out of 21,096,405
Insertions: 405,162 out of 21,096,405
Identity over aligned base-pairs: 77.6%

Block size distribution

Size range All 200,021 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
351
2.2 kb
10 bp - 100 bp
25,088
1.5 Mb
2,039
136.8 kb
100 bp - 1 kb
134,054
57.2 Mb
9,486
3.7 Mb
1 kb - 10 kb
40,384
73.0 Mb
4,744
12.8 Mb
10 kb - 100 kb
144
2.2 Mb
544
14.6 Mb
100 kb - 1 Mb
162
55.9 Mb
1 Mb - 10 Mb
24
46.7 Mb