Anopheles quadriannulatus vs Anopheles maculatus LastZ results

Anopheles quadriannulatus (Anopheles quadriannulatus, AquaS1) and Anopheles maculatus (Anopheles maculatus, AmacM1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 99. Anopheles quadriannulatus 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 quadriannulatusAnopheles maculatus
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 126,417 alignment blocks

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

Uncovered: 194,543,637 out of 283,828,998
Covered: 89,285,361 out of 283,828,998

Uncovered: 3,822,907 out of 21,196,160
Matches: 13,522,329 out of 21,196,160
Mismatches: 3,491,496 out of 21,196,160
Insertions: 359,428 out of 21,196,160
Identity over aligned base-pairs: 77.8%

Anopheles maculatus

Uncovered: 58,545,822 out of 141,894,015
Covered: 83,348,193 out of 141,894,015

Uncovered: 622,847 out of 16,388,885
Matches: 12,503,237 out of 16,388,885
Mismatches: 2,991,860 out of 16,388,885
Insertions: 270,941 out of 16,388,885
Identity over aligned base-pairs: 79.3%

Block size distribution

Size range All 126,417 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
138
856.0 bp
10 bp - 100 bp
10,417
662.0 kb
1,679
116.9 kb
100 bp - 1 kb
80,798
37.1 Mb
15,860
8.2 Mb
1 kb - 10 kb
35,048
60.7 Mb
34,282
85.5 Mb
10 kb - 100 kb
16
176.8 kb
378
4.8 Mb