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Bombus terrestris (Buff-tailed bumblebee) vs Bombus impatiens (Common eastern bumblebee) LastZ results

Bombus terrestris (Buff-tailed bumblebee) (Bombus terrestris, Bter_1.0) and Bombus impatiens (Common eastern bumblebee) (Bombus impatiens, BIMP_2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 106. Bombus terrestris (Buff-tailed bumblebee) 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 terrestris (Buff-tailed bumblebee)Bombus impatiens (Common eastern bumblebee)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 129,696 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Bombus terrestris (Buff-tailed bumblebee)

Uncovered: 7,273,906 out of 248,654,244
Covered: 241,380,338 out of 248,654,244

Uncovered: 29,878 out of 18,548,448
Matches: 17,904,707 out of 18,548,448
Mismatches: 594,874 out of 18,548,448
Insertions: 18,989 out of 18,548,448
Identity over aligned base-pairs: 96.7%

Bombus impatiens (Common eastern bumblebee)

Uncovered: 7,954,894 out of 246,856,484
Covered: 238,901,590 out of 246,856,484

Uncovered: 47,449 out of 18,806,354
Matches: 17,864,666 out of 18,806,354
Mismatches: 870,584 out of 18,806,354
Insertions: 23,655 out of 18,806,354
Identity over aligned base-pairs: 95.2%

Block size distribution

Size range All 129,696 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,013
11.8 kb
10 bp - 100 bp
23,940
1.4 Mb
10,773
675.5 kb
100 bp - 1 kb
60,803
23.6 Mb
32,818
12.9 Mb
1 kb - 10 kb
36,786
127.2 Mb
7,968
19.9 Mb
10 kb - 100 kb
6,154
109.3 Mb
323
9.4 Mb
100 kb - 1 Mb
209
84.9 Mb
1 Mb - 10 Mb
70
133.8 Mb