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Apis mellifera (Honey bee, DH4) vs Bombus impatiens (Common eastern bumblebee) LastZ results

Apis mellifera (Honey bee, DH4) (Apis mellifera, Amel_HAv3.1) and Bombus impatiens (Common eastern bumblebee) (Bombus impatiens, BIMP_2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 106. Apis mellifera (Honey bee, 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 (Honey bee, DH4)Bombus impatiens (Common eastern bumblebee)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 211,029 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Apis mellifera (Honey bee, DH4)

Uncovered: 83,169,424 out of 225,250,884
Covered: 142,081,460 out of 225,250,884

Uncovered: 238,450 out of 18,346,913
Matches: 15,102,371 out of 18,346,913
Mismatches: 2,841,370 out of 18,346,913
Insertions: 164,722 out of 18,346,913
Identity over aligned base-pairs: 83.4%

Bombus impatiens (Common eastern bumblebee)

Uncovered: 102,410,663 out of 246,856,484
Covered: 144,445,821 out of 246,856,484

Uncovered: 530,528 out of 18,806,354
Matches: 15,249,970 out of 18,806,354
Mismatches: 2,806,687 out of 18,806,354
Insertions: 219,169 out of 18,806,354
Identity over aligned base-pairs: 83.4%

Block size distribution

Size range All 211,029 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,402
9.7 kb
10 bp - 100 bp
18,591
1.0 Mb
3,256
232.0 kb
100 bp - 1 kb
148,340
69.0 Mb
17,672
6.9 Mb
1 kb - 10 kb
42,308
86.8 Mb
3,284
7.4 Mb
10 kb - 100 kb
387
5.0 Mb
347
14.6 Mb
100 kb - 1 Mb
1
124.8 kb
326
106.5 Mb
1 Mb - 10 Mb
19
26.2 Mb