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Phaeodactylum tricornutum vs Pythium aphanidermatum LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. 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 tricornutumPythium aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,580 alignment blocks

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

Uncovered: 25,621,987 out of 27,568,093
Covered: 1,946,106 out of 27,568,093

Uncovered: 16,002,580 out of 17,873,974
Matches: 1,109,875 out of 17,873,974
Mismatches: 679,143 out of 17,873,974
Insertions: 82,376 out of 17,873,974
Identity over aligned base-pairs: 59.3%

Pythium aphanidermatum

Uncovered: 33,761,291 out of 35,876,849
Covered: 2,115,558 out of 35,876,849

Uncovered: 16,115,207 out of 18,015,574
Matches: 1,143,519 out of 18,015,574
Mismatches: 685,333 out of 18,015,574
Insertions: 71,515 out of 18,015,574
Identity over aligned base-pairs: 60.2%

Block size distribution

Size range All 5,580 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
45.0 bp
10 bp - 100 bp
669
47.0 kb
186
13.4 kb
100 bp - 1 kb
4,310
1.7 Mb
2,055
995.8 kb
1 kb - 10 kb
593
860.6 kb
930
1.6 Mb