Bombus impatiens vs Apis mellifera (DH4) LastZ results

Bombus impatiens (Bombus impatiens, BIMP_2.0) and Apis mellifera (DH4) (Apis mellifera, Amel_HAv3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 102. Bombus impatiens 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

ParameterBombus impatiensApis mellifera (DH4)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 219,787 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Bombus impatiens

Uncovered: 102,730,580 out of 249,185,056
Covered: 146,454,476 out of 249,185,056

Uncovered: 3,892,848 out of 22,494,304
Matches: 15,432,830 out of 22,494,304
Mismatches: 2,934,758 out of 22,494,304
Insertions: 233,868 out of 22,494,304
Identity over aligned base-pairs: 83.0%

Apis mellifera (DH4)

Uncovered: 83,009,508 out of 225,250,884
Covered: 142,241,376 out of 225,250,884

Uncovered: 247,526 out of 18,346,913
Matches: 15,084,888 out of 18,346,913
Mismatches: 2,849,230 out of 18,346,913
Insertions: 165,269 out of 18,346,913
Identity over aligned base-pairs: 83.3%

Block size distribution

Size range All 219,787 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,397
9.7 kb
10 bp - 100 bp
20,504
1.2 Mb
4,544
325.1 kb
100 bp - 1 kb
154,983
70.7 Mb
23,910
8.6 Mb
1 kb - 10 kb
42,516
87.1 Mb
3,498
7.8 Mb
10 kb - 100 kb
386
5.0 Mb
352
14.6 Mb
100 kb - 1 Mb
1
124.8 kb
326
106.5 Mb
1 Mb - 10 Mb
19
26.2 Mb