Anopheles culicifacies vs Anopheles quadriannulatus LastZ results

Anopheles culicifacies (Anopheles culicifacies, AculA1) and Anopheles quadriannulatus (Anopheles quadriannulatus, AquaS1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 99. Anopheles culicifacies 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 culicifaciesAnopheles quadriannulatus
Chunk size10,100,00010,100,000
Overlap100,000100,000
Group set size10,100,00010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 163,015 alignment blocks

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

Uncovered: 78,081,088 out of 202,998,806
Covered: 124,917,718 out of 202,998,806

Uncovered: 429,189 out of 20,923,336
Matches: 16,013,972 out of 20,923,336
Mismatches: 4,175,267 out of 20,923,336
Insertions: 304,908 out of 20,923,336
Identity over aligned base-pairs: 78.1%

Anopheles quadriannulatus

Uncovered: 151,080,331 out of 283,828,998
Covered: 132,748,667 out of 283,828,998

Uncovered: 586,816 out of 21,196,160
Matches: 16,164,230 out of 21,196,160
Mismatches: 3,978,349 out of 21,196,160
Insertions: 466,765 out of 21,196,160
Identity over aligned base-pairs: 78.4%

Block size distribution

Size range All 163,015 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
246
1.6 kb
10 bp - 100 bp
13,785
852.0 kb
1,741
117.9 kb
100 bp - 1 kb
98,352
45.1 Mb
8,213
3.4 Mb
1 kb - 10 kb
50,406
101.0 Mb
11,545
46.4 Mb
10 kb - 100 kb
226
2.8 Mb
4,348
95.6 Mb
100 kb - 1 Mb
32
4.2 Mb