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Albugo laibachii vs Emiliania huxleyi LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Albugo laibachii 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

ParameterAlbugo laibachiiEmiliania huxleyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,651 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 31,678,316 out of 32,766,811
Covered: 1,088,495 out of 32,766,811

Uncovered: 14,896,929 out of 15,902,867
Matches: 581,526 out of 15,902,867
Mismatches: 397,713 out of 15,902,867
Insertions: 26,699 out of 15,902,867
Identity over aligned base-pairs: 57.8%

Emiliania huxleyi

Uncovered: 166,037,814 out of 167,675,649
Covered: 1,637,835 out of 167,675,649

Uncovered: 38,399,563 out of 39,740,234
Matches: 819,019 out of 39,740,234
Mismatches: 487,039 out of 39,740,234
Insertions: 34,613 out of 39,740,234
Identity over aligned base-pairs: 61.1%

Block size distribution

Size range All 7,651 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
29
145.0 bp
10 bp - 100 bp
1,875
133.9 kb
396
29.0 kb
100 bp - 1 kb
5,548
1.6 Mb
2,666
1.0 Mb
1 kb - 10 kb
198
312.2 kb
547
944.8 kb
10 kb - 100 kb
1
21.6 kb
1
21.6 kb