Anopheles gambiae vs Anopheles minimus LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles minimus (Anopheles minimus, AminM1) 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 minimus
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 176,309 alignment blocks

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

Uncovered: 126,829,022 out of 281,378,673
Covered: 154,549,651 out of 281,378,673

Uncovered: 545,647 out of 22,369,942
Matches: 17,061,380 out of 22,369,942
Mismatches: 4,299,386 out of 22,369,942
Insertions: 463,529 out of 22,369,942
Identity over aligned base-pairs: 78.2%

Anopheles minimus

Uncovered: 69,831,924 out of 201,793,324
Covered: 131,961,400 out of 201,793,324

Uncovered: 357,905 out of 21,001,575
Matches: 16,163,552 out of 21,001,575
Mismatches: 4,196,425 out of 21,001,575
Insertions: 283,693 out of 21,001,575
Identity over aligned base-pairs: 78.3%

Block size distribution

Size range All 176,309 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
328
2.1 kb
10 bp - 100 bp
15,269
943.6 kb
2,516
175.8 kb
100 bp - 1 kb
102,418
46.7 Mb
10,948
4.1 Mb
1 kb - 10 kb
58,029
119.6 Mb
5,037
14.0 Mb
10 kb - 100 kb
265
3.7 Mb
503
11.5 Mb
100 kb - 1 Mb
97
35.7 Mb
1 Mb - 10 Mb
43
105.5 Mb