Anopheles gambiae vs Anopheles atroparvus LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles atroparvus (Anopheles atroparvus, AatrE3) 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 atroparvus
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 172,975 alignment blocks

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

Uncovered: 207,637,718 out of 281,378,673
Covered: 73,740,955 out of 281,378,673

Uncovered: 1,373,609 out of 22,369,942
Matches: 15,595,265 out of 22,369,942
Mismatches: 4,877,464 out of 22,369,942
Insertions: 523,604 out of 22,369,942
Identity over aligned base-pairs: 74.3%

Anopheles atroparvus

Uncovered: 159,275,666 out of 225,295,225
Covered: 66,019,559 out of 225,295,225

Uncovered: 1,310,580 out of 20,693,284
Matches: 14,495,182 out of 20,693,284
Mismatches: 4,344,067 out of 20,693,284
Insertions: 543,455 out of 20,693,284
Identity over aligned base-pairs: 74.8%

Block size distribution

Size range All 172,975 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
205
1.2 kb
10 bp - 100 bp
40,300
2.5 Mb
3,229
211.8 kb
100 bp - 1 kb
113,381
41.0 Mb
10,590
4.0 Mb
1 kb - 10 kb
18,808
36.4 Mb
4,617
13.1 Mb
10 kb - 100 kb
281
4.4 Mb
661
16.8 Mb
100 kb - 1 Mb
142
37.6 Mb
1 Mb - 10 Mb
8
12.7 Mb