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Emiliania huxleyi vs Pythium irregulare LastZ results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_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 irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 21,847 alignment blocks

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

Uncovered: 162,781,471 out of 167,675,649
Covered: 4,894,178 out of 167,675,649

Uncovered: 36,108,790 out of 39,740,234
Matches: 2,289,351 out of 39,740,234
Mismatches: 1,149,882 out of 39,740,234
Insertions: 192,211 out of 39,740,234
Identity over aligned base-pairs: 63.0%

Pythium irregulare

Uncovered: 39,917,298 out of 42,968,084
Covered: 3,050,786 out of 42,968,084

Uncovered: 17,884,969 out of 20,543,058
Matches: 1,612,111 out of 20,543,058
Mismatches: 918,684 out of 20,543,058
Insertions: 127,294 out of 20,543,058
Identity over aligned base-pairs: 60.6%

Block size distribution

Size range All 21,847 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
118
671.0 bp
10 bp - 100 bp
5,365
368.8 kb
1,426
97.5 kb
100 bp - 1 kb
15,592
4.7 Mb
7,723
3.0 Mb
1 kb - 10 kb
771
1.2 Mb
1,763
3.1 Mb
10 kb - 100 kb
1
25.6 kb
2
42.3 kb