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Emiliania huxleyi vs Pythium iwayamai LastZ results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 23,049 alignment blocks

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

Uncovered: 162,385,496 out of 167,675,649
Covered: 5,290,153 out of 167,675,649

Uncovered: 35,889,076 out of 39,740,234
Matches: 2,401,115 out of 39,740,234
Mismatches: 1,237,559 out of 39,740,234
Insertions: 212,484 out of 39,740,234
Identity over aligned base-pairs: 62.3%

Pythium iwayamai

Uncovered: 39,964,413 out of 43,199,174
Covered: 3,234,761 out of 43,199,174

Uncovered: 16,895,799 out of 19,552,457
Matches: 1,628,231 out of 19,552,457
Mismatches: 891,470 out of 19,552,457
Insertions: 136,957 out of 19,552,457
Identity over aligned base-pairs: 61.3%

Block size distribution

Size range All 23,049 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
108
595.0 bp
10 bp - 100 bp
5,484
373.7 kb
1,602
110.6 kb
100 bp - 1 kb
16,660
5.1 Mb
8,654
3.4 Mb
1 kb - 10 kb
797
1.3 Mb
1,818
3.1 Mb
10 kb - 100 kb
1
20.1 kb