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Emiliania huxleyi vs Pythium arrhenomanes LastZ results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Emiliania huxleyi 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

ParameterEmiliania huxleyiPythium arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 21,378 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Emiliania huxleyi

Uncovered: 162,359,626 out of 167,675,649
Covered: 5,316,023 out of 167,675,649

Uncovered: 35,851,047 out of 39,740,234
Matches: 2,399,571 out of 39,740,234
Mismatches: 1,263,944 out of 39,740,234
Insertions: 225,672 out of 39,740,234
Identity over aligned base-pairs: 61.7%

Pythium arrhenomanes

Uncovered: 41,420,257 out of 44,672,625
Covered: 3,252,368 out of 44,672,625

Uncovered: 15,744,270 out of 18,367,184
Matches: 1,577,952 out of 18,367,184
Mismatches: 906,482 out of 18,367,184
Insertions: 138,480 out of 18,367,184
Identity over aligned base-pairs: 60.2%

Block size distribution

Size range All 21,378 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
103
566.0 bp
10 bp - 100 bp
4,775
324.7 kb
1,439
97.8 kb
100 bp - 1 kb
15,617
5.0 Mb
8,263
3.3 Mb
1 kb - 10 kb
880
1.4 Mb
1,821
3.2 Mb
10 kb - 100 kb
3
33.1 kb
4
44.4 kb