Anopheles culicifacies vs Anopheles maculatus LastZ results

Anopheles culicifacies (Anopheles culicifacies, AculA1) and Anopheles maculatus (Anopheles maculatus, AmacM1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 99. Anopheles culicifacies 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 culicifaciesAnopheles 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 114,347 alignment blocks

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

Uncovered: 101,743,085 out of 202,998,806
Covered: 101,255,721 out of 202,998,806

Uncovered: 3,555,465 out of 20,923,336
Matches: 14,043,946 out of 20,923,336
Mismatches: 3,107,150 out of 20,923,336
Insertions: 216,775 out of 20,923,336
Identity over aligned base-pairs: 80.9%

Anopheles maculatus

Uncovered: 41,966,787 out of 141,894,015
Covered: 99,927,228 out of 141,894,015

Uncovered: 514,861 out of 16,388,885
Matches: 13,066,206 out of 16,388,885
Mismatches: 2,553,561 out of 16,388,885
Insertions: 254,257 out of 16,388,885
Identity over aligned base-pairs: 82.3%

Block size distribution

Size range All 114,347 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
197
1.3 kb
10 bp - 100 bp
7,062
457.4 kb
2,284
164.1 kb
100 bp - 1 kb
61,106
29.7 Mb
18,243
9.1 Mb
1 kb - 10 kb
45,966
84.4 Mb
42,650
102.2 Mb
10 kb - 100 kb
16
180.4 kb
269
3.3 Mb