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Pythium arrhenomanes vs Pythium irregulare LastZ results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium arrhenomanes 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 arrhenomanesPythium irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 39,662 alignment blocks

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

Uncovered: 25,058,625 out of 44,672,625
Covered: 19,614,000 out of 44,672,625

Uncovered: 3,912,498 out of 18,367,184
Matches: 9,691,244 out of 18,367,184
Mismatches: 4,270,083 out of 18,367,184
Insertions: 493,359 out of 18,367,184
Identity over aligned base-pairs: 67.0%

Pythium irregulare

Uncovered: 22,988,519 out of 42,968,084
Covered: 19,979,565 out of 42,968,084

Uncovered: 4,647,619 out of 20,543,058
Matches: 10,349,914 out of 20,543,058
Mismatches: 4,826,811 out of 20,543,058
Insertions: 718,714 out of 20,543,058
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 39,662 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
137
753.0 bp
10 bp - 100 bp
4,496
305.1 kb
1,138
81.4 kb
100 bp - 1 kb
27,989
11.4 Mb
9,756
4.4 Mb
1 kb - 10 kb
7,025
12.1 Mb
6,512
16.8 Mb
10 kb - 100 kb
15
192.1 kb
193
2.8 Mb