Anopheles gambiae vs Anopheles culicifacies LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles culicifacies (Anopheles culicifacies, AculA1) 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 culicifacies
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 182,241 alignment blocks

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

Uncovered: 137,864,998 out of 281,378,673
Covered: 143,513,675 out of 281,378,673

Uncovered: 697,876 out of 22,369,942
Matches: 16,972,193 out of 22,369,942
Mismatches: 4,241,056 out of 22,369,942
Insertions: 458,817 out of 22,369,942
Identity over aligned base-pairs: 78.3%

Anopheles culicifacies

Uncovered: 76,976,232 out of 202,998,806
Covered: 126,022,574 out of 202,998,806

Uncovered: 381,251 out of 20,923,336
Matches: 16,039,039 out of 20,923,336
Mismatches: 4,192,734 out of 20,923,336
Insertions: 310,312 out of 20,923,336
Identity over aligned base-pairs: 78.1%

Block size distribution

Size range All 182,241 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
324
1.9 kb
10 bp - 100 bp
16,015
999.8 kb
2,619
182.2 kb
100 bp - 1 kb
110,504
50.0 Mb
12,411
4.8 Mb
1 kb - 10 kb
55,278
109.0 Mb
13,840
51.9 Mb
10 kb - 100 kb
120
1.5 Mb
4,482
99.8 Mb
100 kb - 1 Mb
37
4.8 Mb