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Pythium ultimum vs Emiliania huxleyi LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) 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 111. Pythium ultimum 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

ParameterPythium ultimumEmiliania huxleyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 20,076 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum

Uncovered: 41,810,844 out of 44,913,582
Covered: 3,102,738 out of 44,913,582

Uncovered: 17,301,299 out of 19,826,256
Matches: 1,507,092 out of 19,826,256
Mismatches: 905,081 out of 19,826,256
Insertions: 112,784 out of 19,826,256
Identity over aligned base-pairs: 59.7%

Emiliania huxleyi

Uncovered: 163,142,154 out of 167,675,649
Covered: 4,533,495 out of 167,675,649

Uncovered: 36,334,781 out of 39,740,234
Matches: 2,119,748 out of 39,740,234
Mismatches: 1,114,600 out of 39,740,234
Insertions: 171,105 out of 39,740,234
Identity over aligned base-pairs: 62.2%

Block size distribution

Size range All 20,076 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
73
432.0 bp
10 bp - 100 bp
4,914
334.4 kb
1,331
91.3 kb
100 bp - 1 kb
14,395
4.3 Mb
7,227
2.8 Mb
1 kb - 10 kb
687
1.2 Mb
1,568
2.9 Mb
10 kb - 100 kb
7
140.8 kb
8
190.4 kb