Anopheles gambiae vs Anopheles darlingi LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles darlingi (Anopheles darlingi, AdarC3) 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 gambiaeAnopheles darlingi
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 93,291 alignment blocks

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

Uncovered: 238,226,307 out of 273,109,044
Covered: 34,882,737 out of 273,109,044

Uncovered: 2,108,398 out of 21,237,323
Matches: 14,156,340 out of 21,237,323
Mismatches: 4,467,110 out of 21,237,323
Insertions: 505,475 out of 21,237,323
Identity over aligned base-pairs: 74.0%

Anopheles darlingi

Uncovered: 103,605,898 out of 136,950,925
Covered: 33,345,027 out of 136,950,925

Uncovered: 1,419,080 out of 18,211,055
Matches: 12,265,900 out of 18,211,055
Mismatches: 3,987,223 out of 18,211,055
Insertions: 538,852 out of 18,211,055
Identity over aligned base-pairs: 73.0%

Block size distribution

Size range All 93,291 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
106
582.0 bp
10 bp - 100 bp
30,826
1.8 Mb
5,152
304.2 kb
100 bp - 1 kb
52,190
17.5 Mb
9,087
3.1 Mb
1 kb - 10 kb
10,151
18.9 Mb
4,007
12.4 Mb
10 kb - 100 kb
18
231.2 kb
930
20.7 Mb
100 kb - 1 Mb
12
1.9 Mb