Anopheles gambiae vs Anopheles christyi LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles christyi (Anopheles christyi, AchrA1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 100. 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 christyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 130,385 alignment blocks

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

Uncovered: 115,179,108 out of 281,378,673
Covered: 166,199,565 out of 281,378,673

Uncovered: 629,283 out of 22,369,942
Matches: 18,331,954 out of 22,369,942
Mismatches: 3,094,765 out of 22,369,942
Insertions: 313,940 out of 22,369,942
Identity over aligned base-pairs: 84.3%

Anopheles christyi

Uncovered: 28,099,332 out of 172,658,580
Covered: 144,559,248 out of 172,658,580

Uncovered: 121,658 out of 17,847,860
Matches: 14,897,841 out of 17,847,860
Mismatches: 2,657,917 out of 17,847,860
Insertions: 170,444 out of 17,847,860
Identity over aligned base-pairs: 84.0%

Block size distribution

Size range All 130,385 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
579
3.5 kb
10 bp - 100 bp
10,781
667.9 kb
3,679
262.4 kb
100 bp - 1 kb
59,868
26.8 Mb
17,356
6.7 Mb
1 kb - 10 kb
58,246
144.8 Mb
28,211
98.3 Mb
10 kb - 100 kb
911
12.4 Mb
4,309
78.6 Mb
100 kb - 1 Mb
7
913.7 kb