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Phaeodactylum tricornutum vs Emiliania huxleyi LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) 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. Phaeodactylum tricornutum 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

ParameterPhaeodactylum tricornutumEmiliania huxleyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 11,842 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum

Uncovered: 25,959,591 out of 27,568,093
Covered: 1,608,502 out of 27,568,093

Uncovered: 16,342,973 out of 17,873,974
Matches: 913,286 out of 17,873,974
Mismatches: 567,037 out of 17,873,974
Insertions: 50,678 out of 17,873,974
Identity over aligned base-pairs: 59.7%

Emiliania huxleyi

Uncovered: 164,847,276 out of 167,675,649
Covered: 2,828,373 out of 167,675,649

Uncovered: 37,444,209 out of 39,740,234
Matches: 1,417,122 out of 39,740,234
Mismatches: 800,837 out of 39,740,234
Insertions: 78,066 out of 39,740,234
Identity over aligned base-pairs: 61.7%

Block size distribution

Size range All 11,842 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
55
318.0 bp
10 bp - 100 bp
2,715
190.1 kb
511
37.1 kb
100 bp - 1 kb
8,786
2.6 Mb
4,047
1.7 Mb
1 kb - 10 kb
285
427.5 kb
909
1.5 Mb
10 kb - 100 kb
1
24.4 kb
1
24.4 kb