Apis mellifera (DH4) vs Nasonia vitripennis (AsymCx) LastZ results

Apis mellifera (DH4) (Apis mellifera, Amel_HAv3.1) and Nasonia vitripennis (AsymCx) (Nasonia vitripennis, Nvit_psr_1.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 102. Apis mellifera (DH4) 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

ParameterApis mellifera (DH4)Nasonia vitripennis (AsymCx)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 62,488 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Apis mellifera (DH4)

Uncovered: 203,259,741 out of 225,250,884
Covered: 21,991,143 out of 225,250,884

Uncovered: 4,532,804 out of 18,346,913
Matches: 9,416,034 out of 18,346,913
Mismatches: 4,107,564 out of 18,346,913
Insertions: 290,511 out of 18,346,913
Identity over aligned base-pairs: 68.2%

Nasonia vitripennis (AsymCx)

Uncovered: 273,861,361 out of 297,309,692
Covered: 23,448,331 out of 297,309,692

Uncovered: 8,122,697 out of 22,806,936
Matches: 9,903,349 out of 22,806,936
Mismatches: 4,379,088 out of 22,806,936
Insertions: 401,802 out of 22,806,936
Identity over aligned base-pairs: 67.4%

Block size distribution

Size range All 62,488 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
256
1.6 kb
10 bp - 100 bp
10,368
668.6 kb
3,047
201.9 kb
100 bp - 1 kb
45,857
14.7 Mb
11,572
3.8 Mb
1 kb - 10 kb
6,001
10.6 Mb
4,778
14.8 Mb
10 kb - 100 kb
6
70.3 kb
425
7.2 Mb
100 kb - 1 Mb
1
108.0 kb