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 104. 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 size10,100,00010,100,000
Masking options

Statistics over 110,886 alignment blocks

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

Uncovered: 37,909,839 out of 281,378,673
Covered: 243,468,834 out of 281,378,673

Uncovered: 495,374 out of 22,457,470
Matches: 20,362,461 out of 22,457,470
Mismatches: 1,568,235 out of 22,457,470
Insertions: 31,400 out of 22,457,470
Identity over aligned base-pairs: 92.7%

Anopheles coluzzii

Uncovered: 10,666,415 out of 224,417,174
Covered: 213,750,759 out of 224,417,174

Uncovered: 361,204 out of 19,279,148
Matches: 18,286,314 out of 19,279,148
Mismatches: 611,210 out of 19,279,148
Insertions: 20,420 out of 19,279,148
Identity over aligned base-pairs: 96.7%

Block size distribution

Size range All 110,886 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,415
8.7 kb
10 bp - 100 bp
16,068
902.5 kb
5,761
364.0 kb
100 bp - 1 kb
49,288
19.8 Mb
23,343
10.0 Mb
1 kb - 10 kb
38,018
126.0 Mb
14,683
36.1 Mb
10 kb - 100 kb
6,090
112.6 Mb
1,055
23.5 Mb
100 kb - 1 Mb
7
785.9 kb
82
27.6 Mb
1 Mb - 10 Mb
39
150.7 Mb
10 Mb - 100 Mb
1
12.0 Mb