Anopheles gambiae vs Culex quinquefasciatus LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Culex quinquefasciatus (Culex quinquefasciatus, CpipJ2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 91. 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 gambiaeCulex quinquefasciatus
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 65,311 alignment blocks

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

Uncovered: 250,693,942 out of 273,109,044
Covered: 22,415,102 out of 273,109,044

Uncovered: 4,398,285 out of 21,237,323
Matches: 11,574,255 out of 21,237,323
Mismatches: 4,502,703 out of 21,237,323
Insertions: 762,080 out of 21,237,323
Identity over aligned base-pairs: 68.7%

Culex quinquefasciatus

Uncovered: 554,505,769 out of 579,057,705
Covered: 24,551,936 out of 579,057,705

Uncovered: 7,128,277 out of 24,941,119
Matches: 12,499,040 out of 24,941,119
Mismatches: 4,920,844 out of 24,941,119
Insertions: 392,958 out of 24,941,119
Identity over aligned base-pairs: 70.2%

Block size distribution

Size range All 65,311 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
198
1.1 kb
10 bp - 100 bp
12,476
810.7 kb
5,406
359.7 kb
100 bp - 1 kb
45,895
16.0 Mb
17,827
6.6 Mb
1 kb - 10 kb
6,729
11.6 Mb
7,015
17.5 Mb
10 kb - 100 kb
13
222.2 kb
255
4.3 Mb