Anopheles gambiae vs Anopheles stephensi LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles stephensi (Anopheles stephensi, AsteS1) 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 stephensi
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 187,275 alignment blocks

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

Uncovered: 134,375,243 out of 281,378,673
Covered: 147,003,430 out of 281,378,673

Uncovered: 544,448 out of 22,369,942
Matches: 17,180,723 out of 22,369,942
Mismatches: 4,202,359 out of 22,369,942
Insertions: 442,412 out of 22,369,942
Identity over aligned base-pairs: 78.7%

Anopheles stephensi

Uncovered: 94,899,668 out of 225,369,006
Covered: 130,469,338 out of 225,369,006

Uncovered: 396,509 out of 21,181,416
Matches: 16,382,792 out of 21,181,416
Mismatches: 4,028,833 out of 21,181,416
Insertions: 373,282 out of 21,181,416
Identity over aligned base-pairs: 78.8%

Block size distribution

Size range All 187,275 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
308
2.0 kb
10 bp - 100 bp
17,396
1.1 Mb
2,371
160.9 kb
100 bp - 1 kb
114,077
51.4 Mb
9,572
3.6 Mb
1 kb - 10 kb
55,135
109.1 Mb
4,590
12.9 Mb
10 kb - 100 kb
359
4.6 Mb
784
22.5 Mb
100 kb - 1 Mb
343
112.4 Mb
1 Mb - 10 Mb
10
14.7 Mb