Anopheles gambiae vs Anopheles coluzzii LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles coluzzii (Anopheles coluzzii, AcolM1) 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 coluzzii
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 111,081 alignment blocks

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

Uncovered: 37,933,321 out of 281,378,673
Covered: 243,445,352 out of 281,378,673

Uncovered: 502,369 out of 22,369,942
Matches: 20,219,767 out of 22,369,942
Mismatches: 1,617,247 out of 22,369,942
Insertions: 30,559 out of 22,369,942
Identity over aligned base-pairs: 92.5%

Anopheles coluzzii

Uncovered: 9,126,987 out of 224,455,335
Covered: 215,328,348 out of 224,455,335

Uncovered: 343,849 out of 19,279,148
Matches: 18,297,163 out of 19,279,148
Mismatches: 617,963 out of 19,279,148
Insertions: 20,173 out of 19,279,148
Identity over aligned base-pairs: 96.6%

Block size distribution

Size range All 111,081 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,413
8.7 kb
10 bp - 100 bp
15,852
889.5 kb
5,669
358.2 kb
100 bp - 1 kb
48,999
19.8 Mb
22,709
9.7 Mb
1 kb - 10 kb
38,737
127.3 Mb
15,362
37.3 Mb
10 kb - 100 kb
6,073
112.2 Mb
1,095
24.3 Mb
100 kb - 1 Mb
7
785.9 kb
83
27.6 Mb
1 Mb - 10 Mb
39
149.8 Mb
10 Mb - 100 Mb
1
12.0 Mb